Switzerland is incredibly accessible from Northern Italy (especially Milan), and September is the 'golden month' to visit. The summer crowds have thinned, the weather is mild, and the historic Alpine Cow Descents (Désalpe) begin in mid-September.
For a 3-day trip starting from Italy, the most efficient and scenic route focuses on Central Switzerland.
If you prefer scenic rail over city sightseeing, follow this route from Milan: