I think the Ossuary (in Czech: Kostnice) is very strange place. I was there on excursion with my Basic School class when I about ten years old. I didn't feel very well there.
But it isn't in Prague. Kutna Hora is a town about 60 km east from Prague.
The historical town center belongs to the UNESCO monuments and there are interesting building - for example gothic cathedral of St. Barbara (in Czech: Chram sv. Barbory) which was founded in 14th century.
I think Kutna Hora worth visiting. But there are many other nice places in Czech republic.
You can find many useful information on the official website
http://www.czech.cz/en/ not only in Czech, but also in English, German, French, Spanish and Russian.
If you haven't fear of bones and have strong nature, you can see the official website of that place at
http://www.kostnice.cz/. If you haven't strong nature, you could read about it here
http://www.czech.cz/en/culture/most-beauti...-of-all-saints/ without any photos of skulls.