We are getting requests for pre-finished trim for commercial millwork jobs, and are having problems filling nail holes after pre-finished trim is installed. We usually use a custom stain. Any suggestions?
I've seen lots of moulds glue-applied with a panel adhesive type of product. Doing so with baseboard is especially simple.
Aside from that, you've got the color crayon or filler route. Crayons can match color pretty well if you go to someone like Mohawk (if I remember the name correctly). They make all kinds of advanced touch-up tools, mainly for furniture makers, but good for high-end installations, too. If you're not aware of a company like this, contact your finishing source. He or she will know who to call locally.
1) You can mix different colors together, and if you're patient (and not color blind), you'll get a damn near perfect match.
2) Denatured alcohol is what I've used to wipe the filled spots down. I use a liberal amount so the "haze" doesn't stick around.