Hire the folks who want to do 100% replacement, designed specifically for your space. It's the right way to do it. Or if the 20 K+ price tag is too steep for a fad, leave well enough alone. Wood is classic and never really out of style.

The 3 stair places gave you the correct advice in my opinion. Not cost effective unless it is a DIY project. And even.....................

My question was very specific. I understand that the best way would be to replace the whole staircase, but that's not what I intend to do. I have already ordered the work on the custom wrought iron rail and my question is specifically about the holes on the treads and/or how to add the stringer (who can do this sort of work). If someone could help answer, I would appreciate it. Thank you

There are wood fillers with stain colors out there. Fill holes with wood filler that is close to the stain color. Apply it with a putty knife wider than the hole so you get a flat surface. Sand till smooth. Use more filler if it isnt flat. Sand again. Find a stain that matches the wood. Sherwin williams has good stain matching. Stain the filler to get it closer to the staircase color. Final coat with floor polyurethane for durability.

This will be noticeable because of the lack of wood grains, but only if you look for it. Perhaps you could experiment making faux wood grains before you seal it with poly. http://www.redouxinteriors.com/2012/07/how-to-make-anything-look-like-real-wood/

Of course replacing the treads and matching the stain to the staircase would be best but life aint perfect.

Geoffrey has the better idea to sand the entire top of the tread and then stain the whole top to match the rest of the staircase. Will be a more uniform look and hide the filler well.

wcutiew:

I hope you haven't already ordered an iron railing that looks like the one pictured. A 4" sphere isn't allowed to pass through at any point, including the tread/riser/rail triangulation which appears too large to pass code.

The spots on your treads are going to appear very minor compared to the bright red tag you're about to see.

Veneering over the treads to cover the holes may invite another code violation, as you are only permitted a 3/8" variation in riser height. This isn't just enforced to make homeowners angry. Any deviation in gait while on stairs can be fatally dangerous.

The wood filler and stain is not a good idea and I don't like the stringer idea either, although it would abate your code problem. Buy some Ebony squares and go for contrast.

@Corlett: Do you interject fear and doubt into every situation?

Veneer (why?) a code violation. Fatally dangerous. Wood filler and stain - not a good idea (why?)

Its 6" sphere at tread to rail.

http://www.thisiscarpentry.com/2008/09/19/2009-irc-code-stairs/

How is sanding a tread, staining and sealing it a big deal. It isn't like the entire tread will be made of wood filler lol, just a few spots on the edges where no one will step.

""@Corlett: Do you interject fear and doubt into every situation?"

No. I like to get readers to think about subjects they may not have thought of. People see all kinds of crazy stuff in magazines and think they're somehow okay. Sometimes they are, sometimes they're not

"Veneer (why?) a code violation. Fatally dangerous."

The treads could have a veneer installed over them to cover the baluster holes, but if that veneer created more than a 3/8" deviation in any risers, it would be a code violation because it alters the gait of the person using the stairs. Altering a gait unexpectedly can cause falling which can be fatal.

"Wood filler and stain - not a good idea (why?)"

There is no wood grain in wood filler. Wood filler is fine for finish nail holes, not for large fills. It would be difficult if not impossible to get a wood filler to accept a stain to match and the dimensional stability of the filler and the tread would be so different as to create cracks eventually.

Vith: Thanks for the link.

Generic internet parts aren't going to give you a custom look. Neither will blobs of filler that are always obvious, and fall out with the vibrations inherent with a well used stairs.

There is ONE correct way to do this, and the OP has rejected it. The end results will not be the same as a properly designed and fabricated stair system. Obviously. Joe is right about the potential red flag code violations that could make this an unsellable choice come resale since this is obviously being done unpermitted.

Sophie / Joe: Talk about making a mountain out of mole hill. Generic Parts?? Blobs of filler? Vibrations in stairs? Red Tags - the world is crashing around the OP.

Depending upon how large the holes are (I don't know if they were doweled on not). But for a larger hole (like a dowel) use a plug cutter, glue in the plug, sand and finish.

Fill holes with bondo and paint the treads. Or just use iron ballusters to utilize the existing hole pattern.
If plugs are used, the treads will have to be fully sanded and refinished, there is unfinished wood under the existing balluster locations, not just tenon holes.
Does the newel post for this new whiz-bang railing get bolted to any framing, or is it only screwed into the floor and bottom riser? What covers the existing holes and notches from the mounting of the original newel?
Casey

"Does the newel post for this new whiz-bang railing get bolted to any framing, or is it only screwed into the floor and bottom riser? What covers the existing holes and notches from the mounting of the original newel?"

Casey:

My thoughts exactly, but apparently we are "making a mountain out of a molehill."

Stair redos are some of the most hacked jobs around. Having a DIYer attempt it that doesn't understand the finer points and WHY the rebuilding is the better/only choice only puts this project square into that hack category. Building codes are there for your safety. Ignore them at your peril. You're financially culpable for creating unsafe conditions in your home.

I'm confused as to what about changing from wood rails to iron rail makes it against code??? I didn't say I'm changing the stairs

.Each step would need balusters in order to be code compliant as to the
required spacing. Or you would need to change to a closed stringer
stair. It's easier to just rebuild the whole thing. Or order the correct parts, which aren't as you pictured.

Closed Stringer.

Open Stringer.