Sanding. Lots of it.

That is usually a problem with lighter stains. Dark stains do the same, but are not as noticeable.

The problem is that sanding will also remove some of the stain. And you will need to reapply stain.

And that will probably cause the problem to reoccur.

Solution---and groan before you read further---is to remove the filler, stain, and use paint sticks or filler sticks to match the stain. Then finish.

I actually did that on three windows a customer had tried to do herself. She had the skills to do the trim work, but ran into the exact problem you have.

I simply used a drill bit just slightly larger than the filled hole in a cordless drill on the slowest speed. I did not need to drill to the nail head, but did often. The trick was to be able to control the side movement.

It took an hour to drill out the stuff on the three windows. But, the end result satisfied her.

AS I read it, you filled the nail holes on bare wood, applied a stain (oil base or water base) but as yet, have applied no finish. You have a ring or blotch because the wood filler not only filled the nail hole, but also filled the wood pores around the nail hole.
In this case, my suggestion to you would be to use paint remover to lift out the wood filler, then restain. Your last step would be to fill the nail holes with a colored wax filler stick or crayon after the finish is applied.
I can't recommend any other procedure because you did not provide the specifics like; type of wood; type of stain; if finish was applied; and at what point the filler was used. In other words, I need to know the wood and your schedule.

Omigosh, I cannot believe there is a thread about this problem! About 2 years ago, I had windows in my whole house replaced with unbelievably expensive kolbe windows trimmed in clear fir to match. My (totally wonderful) contractor filled the holes with the same product and every single one is blotched. He finished the windows and the trim with a marine oil, which is beautiful and holding up wonderfully, except for the splotches. Just yesterday I finally took a rag with the same marine oil and tried to rub out the splotches; it made no change at all. I know when he put first coat of oil on the wood, he cut it with mineral spirits, then another coat (or 2, 3 in the kitchen) of the oil straight. Can you suggest what might work on this finish to remove the splotches (short of sanding?) They don't show too much except at night, and with 26 windows - well, that's too much work. (asking him to fix it isn't an option). Thanks for any suggestions.

Paint grade vs. stain grade. Same work but about $20 an hour difference in labor to get it right.

The problem is in the wood/filler UNDER the finish.

I know of nothing that can be used ON TOP of the finish to fix the problem UNDER the finish.

The only way to fix the problem is to remove the problem and replace the area(s) with something that will not repeat the problem.

There are ways some people say will fix this problem. Gel stains(a glorified paint), washes, toners, and glazes. All those producyts have their place and use.

None will fix the problem being discussed, IMHO.

Finishing is much more than slapping on a varnish or lacquer over a stain or dye. Especially when a dissimilar filler is used. Many competent contractors/designers/craftspersons do not know or practice that fact. The results are usually what the OP and you now have.

In my case (see post above), the filler was added after the wood was finished with a marine oil (not a varnish or stain). Nothing is on top of the filler. So I was hoping more oil would dissolve/soften it in the splotches. Since mineral spirits thin the oil, would mineral spirits maybe dissolve/soften the filler?

Aidan, do you mean that the wood colored fillers that cause this problem are only designed to be used if you are going to paint over them? I didn't really understand your reply, except the $$ part. Thanks.

Depending on the final finish it is often far easier to leave the holes alone until all colored finishes are applied, then use shellac sticks (and even permanent markers to 'grain' larger patches) then apply a clear top coat.

It is a large amount of detail work, and often very expensive.

My point is that experience is well worth the price paid. This is case and point. Every finish carpenter started out not knowing the nature of wood, putty, stains, and finishes. We learned by making mistakes, noticing the mistakes, and figuring out how to make it better. All the advice over here is coming from those who have gone through the learning process.

Wood colored fillers are designed to sell and make money, just like everything else you buy. Selecting the right products and materials is what the craft is all about.

Your only option is to dig out the putty. A drill works well for the nail holes. For the putty nested in the wood grain, use a needle, x-acto knife, or seam ripper, to carefully scratch out the discolorations from the wood grain. follow up by sanding and wiping with mineral spirits. The mineral spirits should help you to see any remaining putty.

Tbanks aidan. Unfortunately, we who hire folks like my contractor, who is a wonderful craftsman, is a pleasure to work with, and who goes the extra mile for me, don't know what they know and what they don't. I'm sure he's done this over and over but this time it is more noticeable, or I'm pickier than some. It will be a lesson for him, but I likely will never have new windows installed again, so it's wasted on me. Thanks again to you all for your insights.

Thanks someone2010 for that idea. Who knew there are so many tricks for problems with wood! By artists paint, do you mean like oil paints? Sounds kind of scary, but I could try it on a less prominent window in a spare bedroom maybe. Interesting idea. The windows are finished with polymerized Tung Oil. Do you think paint thinner would still be okay?

You are going to need a coat of clear finish on any paint/shellac stick/etc. type repair to protect the repair and hide the change in surfaces sheen.

Paint thinner will not harm cured finishes, except for removing any wax on the surface.

My finish now is polymerized Tung oil, nothing else. I would assume i couldn't put any kind of other finish on top of that, as wouldn't the oil keep it from adhering to the wood? I appreciate all the sharing of expertise here. Thank you all so much!

Two other proceedures you might consider. You can order felt markers for furniture touch up, on line. You get about ten markers and you can use these to make dots and lines to simulate your wood.
Another technique would be to use a card scraper. This is a thin piece of steel about the size of a playing card. You use this to scrape off the finish and hopefully the filler, then you apply the same finish. Finally you use a wax furniture repair crayon of the appropriate color to fill the nail hole. You may have to use a nail set to drive the nail a little way into the wood and leave a hole for the way filler.

The second to last word in the above post is supposed to be wax, not way.

I have several more ways to fix the problem, but they require more expertise and a higher initial investment. The manner I use depends on what is appropriate on an individual basis.

"I would assume i couldn't put any kind of other finish on top of that, as wouldn't the oil keep it from adhering to the wood?"

The repaired areas will have no finish to protect the repair.

Repairing defects in 'thin' finishes like Tung poil are always a problem, especially if you want to keep the rest of the surface 'as is.'

The best you can usually do is try to conceal larger defects and live with any sheen change at the repairs.

Thank you all again for sharing your expertise. The nail holes are fine, blend in perfectly. Around each nail hole is an area that looks like a fingerprint, where my contractor blended in the putty, then wiped it off, I assume. There is no putty that i can see or feel in the splotches and they only show at night. What it looks like happened was the putty was wiped on and filled the minute hairs of the grain (it is cvg fir)and then when the wood aged and darkened, the putty didn't, although he did use a darker putty so it would blend after the wood darkened some - the holes are a perfect color. I think the posts about just trying to blend a tiny bit of finish darker than the putty to mimic the fir color would work. I think the fir has darkened as much as it is going to. I'm going to try it on a less conspicuous window and see if it's an improvement. If not, I can sand and start over. Thank you all!!

OLd post. But similar to my situation, I used minwax and also DAP plastic wood filler natural stainable, to fill nail holes on VG Fir which I had pre-staind with one coat of Old Masters Oil based wiping stain prior.

I used these products because they stain matched on test wood the best.

Well in my tests I did not notice the same "blotches" at the time

SO now I used the Dap on all the trim and porch columns to fill small nail holes, and I noticed blotching! I was using a wet rag to remove and smooth wood filler, because I did not want to sand the 1 coat Pre-stained wood. Tried using warm water and some gentle cleaners like dish soap and tried denatured alcohol, the only thing that removed it was Olive oil in a small test area, after witch I wiped off excess oil with a wet rag.

The problem is that I have 2 more coats of stain to apply, so I think the Stain will not penetrate properly (to match door) if I go ahead and clean all the blotches with olive oil?

And even if I did clean blotches, I would probably need to coa

t the entire wood surface so that whatever reaction the stain does with the oil residue, it would be matching?

Kind of tempted because it looks so nice on the test area where I used the Olvie oil..

but I may just live with blotches and hope the 2 more dark coats of stain I put on & 4 coats of spar Varnish (Exterior door (facing West in WA State) the blotches will not be noticed?

Any advice appreciated, as I have not stained or sealed over the blotches yet.. so maybe if there is a remedy to remove (besides sanding) the blotches?

Itried sanding on a test area and it looks worse.. I do not want to sand because it will lift the 1st coat of stain that was put on previously..

So its either use something that will remove blotches or just live with them..

Anybody advise? My main question is; should I use Olive oil to clean wood filler blotches? Any other suggestions?

Keeping in mind the oil could effect the 2 coats of oil based stain I need to apply after?

Following that with 4-6 coats of spar varnish (exterior door facing west with sun exposure)

As this is a 9 year old thread, two solutions:

I would suggest that one put a piece of painter's tape down and nail through it, then add whatever filler. That way, there's no overflow. "Stainable wood fillers" will take stain, but seldom the same color as surrounding wood. For one reason, every wood takes the stain a little differently.

But I would suggest, too, do the staining, add a coat of finish, then match the color before the final coat of finish.

Also have a similar situation. All nail holes and seams were filled and are lighter colored after one coat of stain. Suggestions? I see sanding it down , mixing stain w the filler. Using stain pens to mark the spots. Just soaking the heck out it w the stain, which is a dark stain btw... dark walnut Minwax. The nail holes have a small spreader swipe mark around them as well, and there are 3 seams approx 2 ft in length
Really like the idea of nailing thru paint tape and then putty, but I’m past that step. Will use on all future projects tho, so thank u for that!!

After a ridiculous amount of research I come across this old thread and it amazes me as I'm from Africa that the products here just don't meet the needs or the expertise offered is really no expertise at all and the experts are even taking a guess.

What I have to offer is really no great solution but it sort of works. I mixed some of the wood sanding from the project with a little stain and a little wood filler, less filler, equal stain and sandings... it's the closest I've come. Hope this helps someone.

Why is DIY so difficult in USA! And contractors who do bad jobs anyway, so expensive?
Mind boggling!