How to best fill holes in drawer face to install new hardware?

I like to up cycle old furniture and sometimes need to change out the hardware for a different size. My problem is that whatever product or technique I use to fill the old holes, they always seem to be noticeable. I have tried a few different brands of wood filler, water putty, tried filling the hole with a dowel so the filler doesn't shrink later--of course I sand whatever product to surface level, but the holes always seem to leave a ghost image...maybe I am too picky, but are then any hints or tricks?
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