Clean the surface real good and then hit it with 400 grit or finer sandpaper.  It least that is what I have done.

you have to be careful with the heat setting too - because the epoxy does not let the heat dissapate - you will end up with a lot of shrinking in one area if you leave the iron on there too long - also - the heat weakens the bond of the epoxy - so less is more when it comes to applying it.

Proviously, I have coated the epoxy with balsaloc or PVA glue to give the "cote something to tack to at a lower heat setting......

I do this on the RC planes alot where I use Epoxy and nylon tape for a wing joint. After sanding the epoxy smooth with a block sander , I use spackle compund and rubb it with a credit card over the sanded epoxy area and use spackel to blend the edge where the epoxy ends and wood begins. it turns out nice but like they said: Use lower heat and go slow small areas... it'll turn out fine! good luck.
\Terry