If the scratches are relatively minor the first thing I try is to use a very large area light source for exposure.
The usual method of putting a contact frame on the baseboard of an enlarger involves a very small intense light source; the stopped down enlarger lens. Small specular light sources accentuate sharpness but they also accentuate negative defects.
For the opposite effect I wire my light table to the enlarger timer and scoot the face down contact frame around on it for the duration of the exposure. Scratches are significantly suppressed. The difference is like the difference between point source and diffusion enlargers.