Suggestions for train trip from Varenna on Lake Como to Paris with 2 nights in Switzerland

From Varenna there is one obvious route, the Bernina Pass route.
The Glacier Express is an extra train, you can still take the regular hourly trains on the same route.

The line from Milan to Varenna continues to Tirano. There you cross the town square to the Rhb station, and take a train over the Bernina Pass to Pontresina and Chur. One or two nights in Pontresina (or other places), then continue over the Glacier Express route to Zermatt. Two nights Zermatt and on to Paris via Geneva or Lausanne.

Thanks for your response Chris. I've actually been on the Glacier Express and would like to travel through an area that I haven't seen. Since we have only a couple of days to get to Paris and the other couple hasn't been to Switzerland, I thought we could take the train to Luzerne, spend the night, take another train to Lusanne for a night and then on to Paris. It could work for other cities as well. Or posibly two nights somewhere in the high Alps rather than the cities mentioned. The train would deliver the best scenery and the two nights would give at least a taste of the culture. Does that seem feasible?

Technically your idea of one night in Luzern and one in Lausanne works, but it leaves you very little time to enjoy the cities and will make you spend a lot of time on admittedly scenic trains.
I would take the Bernina Express route to Luzern, which is a very long but very scenic journey via Tirano, St Moritz, Landquart, and Thalwil near Zürich, taking most of the day. Then spend two nights in Luzern before heading to Paris via Basel. If so inclined on a good weather day and if not "train-ed out", you can head to Mt Pilatus or Mt Rigi during your day in Luzern.

From Tirano, take the Bernina Express. https://www.rhb.ch/en/panoramic-trains/bernina-express Sorry - redundant answer but it was delayed overnight from posting. Just another Bernina vote.