Hi Dave, I think the remaining chunks should dry up with everything else and you'll be able to pick it out. If it doesn't, you may not have let it ferment long enough (I did mine for about five days, which worked great for separation but also caused bug problems). I also used a rough wire colander when I rinsed the seeds. Hope this helps - good luck!

Thanks millyjean,
I did use a colander. A lot did come off but not all.
I fermented for 5 days. I once did it for 7 days, but the seeds started to sprout. Lots of mold grew on top so I know they were ready.

This trick has worked well for me. After the tomato seed has been fermented, I pour the contents into a blender, add water almost to the top, and pulse several times at the slowest speed. This breaks up any remaining pulp & gel sacs. After blending, the good seed settles to the bottom, and the debris pours off easily. Processed this way, the seed is very clean.

The blender was purchased used from a thrift store, and the blades ground half-dull; I use this blender only to process wet seeds.

A blender?

Yup. Works like a charm. Small seeds like tomatoes are seldom damaged; the dull blades are just insurance. Obviously, you don't want to over-do it... only a few seconds at the lowest speed. I process eggplant, ground cherries, tomatillos, gilo, and litchi tomatoes in the blender also, after they have softened.

But if you are apprehensive about using a blender, you can also beat the fermented mixture vigorously with a wire whisk, or with an electric mixer. That is my method of choice for fermented cucumber seed, and for cleaning unfermented squash & melon seed.

None of this beating and blending of seeds has caused your seed to not germinate when planted? If it has, please give percentages. Thanks!

~Angela