I have generated two scripts (schema only), one for all the tables on test database and one for all the tables on prod database. Is there any tool where I can pass in both the scripts and tool will list out all the differences?
Any file comparison tool should work - I use Beyond Compare (http://www.scootersoftware.com/).
If you are really looking at comparing the schemas between two databases - I would recommend downloading and testing RedGate's SQL Compare (http://www.red-gate.com/products/). It works very well and can easily identify differences between environments.