There are direct trains from Amsterdam to Berlin and from Berlin to Prague, so train travel would be fairly easy. If you don't want to take a train all the way back from Prague to Amsterdam you could always book a one-way flight -on Easyjet . It is quite a good airline to fly with.
You can plan 3 days for Prague , 2 days for Berlin and 3 days for Amsterdam . If you are visiting Amsterdam anytime between March end to mid May you can keep one day for Keukenhof garden (Tulips)