Excite the system (black box model) with an appropriate inputs and then use the system identification toolbox to find the appropriate model. You can identlfy the model in state space form, etc. However, you need to provide the order of the system and then verify the fitness percentage of system (black box model) and the identified model. If the fit percentage is very less, try exciting the black box plant with different inputs or change the order of the identifed plant.
One of the best example of uasage of sysid is given in below link: http://www.mathworks.com/products/sysid/demos.html?file=/products/demos/shipping/ident/iddemosl.html
Cheers Bhachku
