I have two feature classes, one that contains all counties for 5 states and the other contains 90 polygons I need clipped only to their pertaining county boundary, but they overlap/ cross the county boundary (See image below). Both feature classes have a field with a unique 5 digit ID for each county as well. Being that I am relatively new to Python, is there a way I can use a loop or searchcursor to clip each of the 90 polygons to their respective county boundary using their 5 digit ID?
*The red rose colored polygons show the overlapping polygons I need to clip and the tan colored polygons show what I need the final product to look like.

where_clause? Iterate over each 5-digit id and pass that to MFL on the red and tan layers, clipping as you go. – Paul Dec 04 '15 at 19:37