Here's a good tip to minimize the work of filling nail holes.
After I install the trim and set the nails, I use masking tape to keep the putty only in the nail holes. To do this, I start by loosely adhering some small strips of tape to a piece of scrap.
Then I use my nailset and a hammer to punch through the tape and into the scrap. When I peel the tape off, the center stays stuck to the scrap, leaving a hole in the tape the same size as the nail hole in the trim.
Next, I position the hole in the tape over the nail hole in the trim and stick the tape down. Now the putty will just fill the nail hole without filling in the wood grain around the hole. Once the putty dries, I just peel off the tape. It eliminates having to sand off excess putty.