If you're planning to visit the 'Isole Borromeo', you'll have to take the train to Stresa. From the station, you are just a 10 minutes walk to the ferry port.

The station of Stresa it's quite small with only a couple of platforms.

If you're coming from Milan, it will take you about 1:30 if you take the train from Stazione di Porta Garibaldi or 1:10 if you take the train from Milano Centrale.

There's also the 'intercity' train, but it's more expensive compared to the regional train.