I propose 2 ways to proceed. One is to learn from evolutionary history of biological systems on how biological clock is made. This approach has the advantage of learning what sort of biochemistry may be required for building a clock. The other way is to learn from human engineered clock to see what internal design features they have.
Circadian clock (http://www.openwetware.org/wiki/BIO254:Pacemaker)
Cryptochromes define a novel circadian clock mechanism (http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0060012)
Cyanobacterium Synechococcus elongatus (PCC 7942): a model organism for a prokaryotic circadian clock (http://www.bio.tamu.edu/FACMENU/FACULTY/GoldenS.htm)
Pendulum clock (http://en.wikipedia.org/wiki/Pendulum_clock)
Digital clock (http://electronics.howstuffworks.com/digital-clock.htm)