Not going to happen, a small patch of putty maybe but the amount your describing never. And the first three guys were correct, there should not be filler there. This is wood, it has to be able to expand and contract and the putty will look worse before it will ever look better.

"All 3 flooring specialists that gave me quote said not to put filler in between the boards as the boards will expand and the filler will eventually look like kitty litter. Okay, fine, I like the "natural look". "

Why didn't you hire one of these guys?

Not all floors are candidates for filler between boards. Those that are filled look best when care is taken to match the filler color to the coated wood. Obviously your finisher failed to do that.

A permanent marker of some kind can be used to color the offending lighter color filler. Once you find a supplier (not all office supply places have a full color line), you may need to use two or more colors to get the result you're after. Fixing this is going to be tedious and will require patience and some artistic skill. If you do this, practice in a closet or other location in the floor, such as where a piece of furniture will cover, for example. Once you've mastered a particular technique, then you're ready for the job. I've done this on some jobs to disguise vivid filler and I know it can be a PITA.

Good luck.

Thanks for your responses. I asked to be e-mailed replies but clearly that didn't happen!

Anyway, the flooring contractor that i hired did originally say that he wouldn't put filler in the floor (he was one of the 3 quotes). In the contract he said that he'd "patch and repair" but I didn't realize that that meant puttying everywhere. Not sure why he decided to do it.

glennsfc - do you have any recommentations on permanant markers? I've tried the Rejuvinate markers and the black looks okay (in between boards where there is already some black from previously discolored putty I imagine) but all other colors seem to show as red.

I'm almost ready to put down lots of rugs :(

Can the filler be removed? There are 2 coats of oil based poly on there.

I have seen professionals use rope dipped in closely matched stain to fill gaps.

Going with filler or not is not the issue, your floors will not expand that drastically to push the filler out, the correct way would have been to fill the entire floor after the first sand process before the fine sanding is done, the key is to use the right filler, (woodwise brand is the only one I use), which with pine would be something like red oak filler, from what you're saying it seems like he probably used white oak filler which definitely stands out from pine, I'm currently refinishing 100 year old pine and after the initial sanding, i will use a trowel over the whole area, even after the second one if needed, that way, when the final sanding round with 100 grit paper is done and screened with a buffer, it will all be smooth and blend in perfectly, and yes, going natural over any wood with poly, it will turn yellow, water based sealer is needed if you want a more natural look.

Dallas- doing the same task here, restoring 100-year old heartpine floors on a house in Louisiana. Not having used woodwise filler brands before, I'd be interested for your opinion on how to attempt to match heart pine since it's such a deeper hue than typical fresh-milled pine boards? Perhaps you have a similar experience to share based on your comment above?