I have rough sanded a 60 year old fir floor.
There are blotches in the bare wood that will not sand out.
Is there anything that can be done to minimize the appearance of the blotching?
I am not planning on staining, just applying a clear finish.
Thanks for your help!

Basically, no. I have done many of those old fir floors. Those blotches we call bruising and cannot be sanded out. Replacement typically doesn't work as new wood doesn't match old. All you could do is use flooring from another part of the house not being refinished to patch the areas were the bruising has occurred.

Gary, thanks for your reply.
I guess we will have to embrace the look of the bruising.
This is flooring I removed from a house about to be demolished so hence no extra for patching.