Translation:František is Matěj and Žofie's father.
I think it's a bit more subtle than that, as it depends on context which you don't have when translating an individual sentence. If Matěj and Žofie are known to be siblings, then "František is Matěj and Žofie's father" is what I'd say too, treating 'Matěj and Žofie' as a single entity. However, if they are not already known to be siblings, then "František is Matěj's and Žofie's father" establishes the relationship for each in turn (probably with stress on the 'and' if spoken).
Is the latter emphasis implied by the Czech word order, perhaps?