If you are coming from Rome… make a stop in Lugano - very beautiful!
Other option would be from Milano to Tirano and then via the Bernina railway to Chur (super train trip!), but then you are already very close to Austria and would have to make a little detour if you wanna travel around Switzerland also.

From Lugano you could go to Locarno and then use the Centovalli Railway to Domodossola. From Domodossola you can go to Brig and further to Spiez (best by mountain railway via Kandersteg than by base tunnel). Spend some time at Thuner See. Take a train from Interlaken to Luzern (Brünig railway). Enjoy Luzern and maybe go up Rigi or Pilatus. Then to Zürich. From Zürich take a train to Innsbruck in Austria and spend some time there (Railway line along this route is also very nice!). From Innsbruck head to Salzburg. Then either go to Vienna or go to CZ (Ceske Budejovice). You could go to Cesky Krumlov and then head from there to Prague.

Thank you.  That all sounds lovely. 

If you want a more detailed suggestion would be helpful to know the duration of your trip and also what you prefer - small cities or big; interests in moutains&nature and also what kind of activities you wanna do on the road (museums, …….)

Duration will be about 10 days.  Smaller cities preferred.  Mainly sightseeing.