The process I use goes something like:
Like some have suggested put some tamiya tape on either side of the join to protect details, then put the putty on, sand, remove the tape then sand with a finer grit. Put on a little extra to account for shrinkage. I use tamiya basic type, Mr Surfacer 500/1000, or one of the various squadron putties.
To remove heavy areas you can use a #11 blade. Drag it backwards to remove some excess but don't go too close to the actual plastic or you could gouge it out. After that i use a coarse stick to get it closer then a medium to get it down to the tape, then remove the tap and clean up with a medium/fine. You can also loosen/remove the putty with Tamiya lacquer thinner. In my experience, it works a little more efficiently than acetone/nail polish remover. You can also use the lacquer thinner to thin the putty to a more watery consistency (a.k.a. homemade Mr. Surfacer) and use it on thin seams that you don't want to overload with thick putty.
Not sure if you know about the wet sanding process but basically you start with a medium or fine grit. Dip the stick in water with a couple drops of dish soap then go the opposite way of your last dry sanding. Go down a coarseness and repeat until you get to the polishing stick. Use that in circular motion to smooth it. You can use plastic polish after that if it still looks a little rough.
Hope that all helps.
Cheers!