Train ride through the Alps

Yes. Since about 50% of Switzerland is the Alps (the southern half) there are many many rail routes through the Alps. Which one is best for you depends on which fits in with your planned itinerary. Assuming you are travelling by train, getting to and from where you are visiting will involve Alpine rail routes.

This rail map shows all the rail lines in Switzerland in red: https://www.sbb.ch/content/dam/sbb/de/pdf/geschaeftsreisen/reisen/Uebersichtskarte_Synoptic_Map_2018_einseitig.pdf
Everything south of a line approximately Lausanne - Bern - Luzern - St Gallen is the Alps

There are 3 rail routes which are marketed as tourist routes:
1) Golden Pass Route. Montreux - Zweisimmen - Spiez - Interlaken - Meiringen - Luzern
2) Glacier Express Route: Zermatt - Brig - Andermatt - Disentis/Mustér - Chur
3) Bernina Route: Chur - St.Moritz - Tirano.

We have ridden all three routes mentioned by Chris F on the regular regional trains, not the designated tourist trains with special cars. Our favorite for scenery is the Bernina Express from Chur to Tirano. We did not do the bus section from Tirano tomLugano.

I've spent time over several journeys covering all the track of all three of the routes, and their side routes, over several years. Except for the Bernina route which we only broke into three days at one time I've never done one end-to-end, preferring to just spend a few hours at a time getting to know a region better. I've seen the fancy named tourist trains but never ridden on them. I much prefer to hop on and off the local unnamed trains which ply the route hourly. They go the same places, stop at all the same stations (and a few that the fancy trains stop at but don't open their doors while the train from the opposite direction passes them or vice-versa. They are much cheaper too. They don't sell wine in angled glasses and they don't have fancy restaurant cars (or any kind of food cars), but for a planned trip I bring planned food from supermarkets. Picnics at supermarket prices. Then again, I'm cheap.