First, you don't estimate the "model", but its parameters. You can then try tests that check if the specification is correct and if you do want to test the "model". 

There are different approaches to estimation. In this nice article the author uses a VAR model to estimate the parameters of the Mundell-Flemming model for the Australian economy. 

http://cms-content.bates.edu/prebuilt/huh.pdf?origin=publication_detail