You can buy a Germany Railpass and a Prague Excursion pass for the travel you described from Berlin to Prague to Munich and Frankfurt. Your German railpass would cover the cost of the ticket from Berlin to the German/Czech border, and your Prague Excursion covers the ticket from the Czech border to Prague.

As an alternative, you should also look at getting a Eurail Select pass with three countries. Even if you are just using Germany and Czech Republic, it may end up being cheaper than buying separate passes for each country (you'd have to select a third country for your pass - but that might be useful anyway as it gives some flexibility if you want to to an excursion to say Austria or Amsterdam or something). Without knowing more specifics on your trip (whether you're under 26, looking for first or second class, etc) I can't say definitively which option will be cheaper.