Sounds like your saddle is too high, but here are some guidelines. What you really want is about a 30 degree bend at the knee when you're foot is at the bottom of the stroke, while pedaling. Your leg should not be nearly at full extension.

One way to insure this is to set the saddle so your foot is horizontal, with the leg fully extended at the bottom of the stroke. During normal pedaling, it only takes a 2-3cm rise of the heel to create the 30 degree bend at the knee. If you pedal with no heel rise, then the saddle would be even lower.