Black "dots" on wooden stair treads, can't sand them away

Question

I am quite a beginner as far as diy is concerned and I'm in the process of refurbishing the old wooden stairs in our new house. Never done that before. It was carpeted so I removed it and there were several layers of paint underneath, and I removed that too, now I am sanding the treads.

The next step would be to stain the treads with a dark colour (to contrast with our flooring which is a clearer colour).

My issue is that being old stairs they have black "dots" and sanding does not seem to remove them, they are not superficial, they have a bit of depth to them, see pictures:

I'd like to know if it is OK to leave them as they are, given that we want to stain with a dark colour. Or is it bad practice and they have to somehow be "cleaned", if so, how?

On an aesthetic view, would leaving them look nice and authentic/rustic, or would it look like amateurish work?

I think I will need to use a stainable filler to mask the nail holes, will the filler be good enough to mask these black "dots" too?

Answer 1

The wood does look like it's either Pine, Hemlock or Fir, all of which are soft and stains tend to be absorbed very easily - much further than you would want to remove material. I have two suggestions:

1) Test the stain you want to use on the bottom of the stair tread. Per the comment from Ashlar, stains are also absorbed and quite frequently look blotchy on those species, especially if you are using a dark stain. You'll want to use a sealer first, which will control the absorption and even it out.

2) Depending on the age and style of your house, I'd go with rustic look and embrace the stains. You will never be able to remove them, as the stains and dings look like they are far below the surface (2mm-6mm). It would take a very dark stain to blend in with the marks and you would be sanding/scraping/planing for a long time to make them look anything other than sturdy old steps.

Personally, I'd put a poly finish on it and show off the grain and rustic nature of the steps. Even if you have a 5-year old house and these are just the product of getting overly beat up, trying to cover them up and look nice is a bit futile. You could paint them, but paint wears off and requires periodic re-painting.