While it seems like such a waste, I've been told not to use them in any canning endeavors, as the damage goes deeper than the eye can see. It's been my experience that plum tomatoes are especially prone to BER and it usually clears up later in the season, barring watering or rain issues. Not sure where you are at in your season. Lori

It will be a lot of work and energy expenditure for a poor quality end product. Sure you can cut off the bad end but the bacteria is distributed throughout the whole fruit and flavor is affected. If you use them in a fresh eating recipe you can disguise the taste but if canned over time on the shelf the flavor and quality declines. So canning is not recommended.

Dave

Ah, good to know. Darn! I'll find some other use that isn't going to be harmful, maybe chopped and roasted on a pizza.