Any decent hotel will let you store your bags in their storage room, so you could leave then at the hotel, and then pick them up before heading to your flight.

While I like the idea of Prague by night (and have some photos from my trip last year), I think I like the idea of staying at the aiport better, and just spend the day in town.

BTW, the bus / metro works great. After staying in town for a couple of days I wanted so save some money and used points for Holiday Inn at the aiport and wen to / from town each day.

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