Define "imperfections". Are they tool marks in the timber? Dents or scratches?
Tool marks = more sanding. Dings, dents, scratches = filling then sanding.
Whilst basswood typically doesn't require grain filling, if you have dings or dents (from transport or manufacture) you're usually better of filling them than trying to sand them out. Spot-sanding a ding or dent will only lead to other problems by creating an uneven surface.
You may just need to sand flat like Simon suggested and re-apply the primer. I've had bodies that required doing this a couple of times before I got a nice flat primed surface.
Also using a "primer surfacer" works well as it has quite a high level of solids in the mixture and is intended to "fill" to a certain degree.
That said, it is not a substitute for grain filling or for fixing dings.