Use of Italian Rail Pass to Smaller Towns

Sure, but why? Those will be Regionale trains which are very cheap. It is not cost effective to use a rail pass on Regionale trains. If you have not purchased the pass, then you need to review the cost effectiveness of the pass.

I think you should rephrase your question. I think you mean "do Siena and Pisa have railway stations?"
The answer is yes, assuredly, they are big towns (PIsa population 88,000, Siena 53,000). I would guess 99% of towns in Europe with populations over 50,000 have stations, and probably most towns of 10,000 also have stations.

The Italian rail pass is valid on all trains, but, as the previous poster said, regional (local) trains of the type that serve towns of this size in Italy are cheap. It is usually cheaper just to buy tickets on the day than to use up one day of an expensive pass. For example Florence (Firenze S. M. Novella) to Siena takes about 1½ hours, one train per hour and costs €8.70.

You need to go to the Italian Railways website http://www.trenitalia.com/ to lookup times and prices for these trains.

There are a few private lines in Italy on which a rail pass of any sort is not valid - among which are the Circumvesuviana, the TreNord trains around Milano, and a number of the lines in the south of Italy.

The lines you are asking about are not on that list - your pass would be valid if you are using a pass-day.

But an Italy pass is from around $60 to $95 US per day of use depending on how long the pass is. These regionale trains will get nowhere near that price - you would be wasting money.

Read what the creator of this website says on his page on Italy passes, http://www.ricksteves.com/travel-tips/transportation/trains/italy-rail-passes#italy

quoting:

Are rail passes a good value for Italy?
Not for most people — think carefully before buying a rail pass, especially if your trip doesn't extend beyond Italy. Most train travelers in Italy spend each rail-travel day taking relatively short rides on the Milan–Venice–Florence–Rome circuit. For these trips (most of which cost less than $60 for a second-class ticket), it's cheaper to buy point-to-point train tickets than a rail pass (since most cost more than $60 per day).

"Extra" travel days on the Italy rail pass cost closer to $20-25 per day, but the higher price for the first three days is the first "hurdle" in the price comparison.