Depends on how bad the seam is, I think puttying and sanding it will be your best bet.
After that lay down a coat of primer and start painting.
There are a few fixes that you can do to get rid of those pesky seams, BUT you will need to do them prior to joining the parts.
Those seams are one of the reasons why I avoid plastic figure kits and go for Vinyl or Resin figure kits, at the most I got to deal with a mold line there.
Think I still got the Kaiyodo Darth Vader lurking in the Pile somewhere, he is waiting for a new clear blade to his lightsaber..
If you plan on working a LOT on figure kits best get yourself a good set of files(diamond files, etc), basic scupting tool set, some wire loops, etc.
P.S.: Feel free to drop me an e-mail to ask figure specific questions.