Screwed up casing staining with filler

OK, I already screwed up by filling all my nail holes with minwax wood filler BEFORE staining. However, I have only stained one isolated window (of 8). The splotchy, crappy look of the first stained window gave me impetus to research, which of course yielded negative results. My question: can I salvage the remaining windows by sanding the crap out of the filled areas before staining? If not, is there any other way I can avoid the chicken pox effect o this?