The marks most likely look like heavy dust or debris on the negative rather than something you should scrub aggressively. Don’t use a lot of pressure, since that increases the risk of scratching the film.

A safe approach is:

1. Clean the negatives gently using standard film-cleaning methods.
2. Rescan and see how much improves.
3. If your scanner or scanning software offers dust-removal, use that.
4. For anything left, retouch the scan with a spot/healing tool in software like Photoshop, Lightroom, or GIMP.

If the marks don’t respond to gentle cleaning, they may be more stubborn contamination or physical damage, in which case digital cleanup is usually the practical solution. Unfortunately, if an entire roll is affected, retouching can be tedious, but it’s often the only way to fully remove the spots from the final images.