Yes, just slowly file until it fits. Once the fit is right, mount the scales and file/sand/grind off the excess scale material.
TIPS:
1) When mounting the scales, a neat trick is to glue on one scale first. Then drill the pin holes from the tang side. Next, glue on the other scale and drill it from the previous holes on the first side. This pretty much guarantees that the scales will fit tight to the bolsters and the holes will align.
2) Don't clamp the scales tightly when gluing up. This would force out all the epoxy and make the joint weak. Use the smallest/weakest clamps you can find and only two clamps
3) Don't rush things. Take your time fitting the scales and when you glue them up use slow cure epoxy. 1 hour cure minimum, and 24 hour cure is even better. Let it cure overnight before doing the next task. Work slow on finishing and shaping the handle. It is easy to take a bit more off ... it is impossible to add it back.
4) The solvent for epoxy before it cures is alcohol. After it cures, only acetone will dissolve it. The best way to avoid getting epoxy on the blade is to tape it up. Any that gets where it won't be sanded away later should be wiped off with alcohol before it hardens fully. Check for squeeze out and wipe off as needed a few times while the resin is hardening. Once hardened, try to sand/scrape/trim away most of the excess before using acetone.OP