I will fill any gaps (not holes) at this point, and it would be best to use dark filler if the floor will be darkly stained. Wood filler in any gaps will crack out eventually, and the floor will look better in the future if the filler is dark all the way through. New floors should have few if any gaps, and an older floor to be stained should be in quite good shape also, so this would be a minor filling. I like to use the new latex fillers is those tubes, it allows you to squeeze the filler deep into those gaps. I never use those poorly adhering trowelable fillers in those big tubs.
Continue sanding now with 60-grit sandpaper, and go SLOWLY with this paper, with medium tension on your drum. You might at this point consider using Aluminum Oxide (ALO) sandpaper for this-grit, as the ALO-grits are a bit more rounded (than silicone carbide), so the wood will be less grooved. This is the most important paper, as it alone will remove all the deep grooves that the coarse paper created. On dense closed grain woods like cherry or maple you must remove all the coarse grain sanding lines. They will never be disguised no mater how many coats of floor finish you apply. Whatever you do NEVER skip this vital medium sanding.
If you want to start with 40-grit (good idea on cherry and maple) on new floors, that's fine. But in this case be sure to sand with 60 and then 100-grit sandpaper. Ignore this at your peril. I see a lot of badly sanded floors, done by paid professionals. Smoothly sanded floors wear better, because there are no high spots (sanding ridges) to wear off first.
When sanding a room there will always be a long sanding run, and a shorter run to finish up the other side. I want you to always to reverse the long and short run for each-grit of sandpaper. This avoids the possible creation of a overlap mark as you wrongly repeat the same sanding pattern. These slight marks across the whole width of the floor will show up only when you stain the floor, and by then it will be too late.
Step 1: How To Sand Wood Floors: Without Leaving Machine Marks Introduction
Step 2: How To Sand Wood Floors: Can it be Sanded?
Step 3: How To Sand Wood Floors: Start with Fine Tuning Your Drum Sander and Choosing the Best Sand Paper
Step 4: How To Sand Wood Floors: The Right Sand Paper Makes The Job For The Initial Rough Sanding 36 Grit
Step 5: How To Sand Wood Floors: Repairing Gaps and Second Sanding Stage With 60 Grit
Step 6: How To Sand Wood Floors: Final Drum Passes with Burnished 80 Grit or Regular 100 or 120 Grit
Step 7: How To Sand Wood Flooring: Edging - Using The Edger Without Effort
Step 8: How To Sand Wood Flooring: Screening and Final Preparation For Staining or Finishing