If you go on the DB site the standard price they quote Munich - Prague (No bahncard etc etc) is EUR 49.
You CAN go Inter City with a change in Nürnberg but that is more expensive.
The EUR 49 is the price on the 2 daytime trains direct Munich-Prague.
They both count as "local trains" in Germany even though they do have catering so you can use the Bayern Ticket.
The 1644 departure (arrive Prague 2245) would cost you EUR 15 (Bayern) and EUR 7 (guestimate, Czech Republic) giving you a price of EUR 22
The morning departure is really crap to use weekdays as its at 0644 and you can't use a Bayern Ticket before 0900 Monday-Friday.
Standard price (no Bahncard etc) to Furth in Wald and then the Czech section would be about EUR 39
Of course Saturday and Sunday and public holidays you can travel on that 0644 departure, arrives Prague 1245.
There are other departures of course during the day on local trains that you might use during the week to get the EUR 22 price but these will require changes in
A ) Regensburg / Furth-i-Wald / Domazlice / Plzen.
or
B ) Plattling / Bayerisch Eisenstein / Klatovy (possibly) / Plzen.
and the time taken would be 7 to 7 and a half hours.
Both the 2 daytime return trains don't reach Bavaria until after 0900 so can always use a Bayern Ticket (ones purchased in advance from MVV ticket machines as they aren't dated)
If there is more than 1 person travelling of course it gets cheaper cos you can use the group Bayern Ticket.
Anorak City or WHAT !



