"Window based exe"? You must be joking. It makes no sense whatsoever. Just forget about it. Better yet, just thing about it a little. Do you know what server side and client side do? It you thing about it, it should be apparent to you, too.
You can only take the source code from your Windows based application and use it in new project, a class library or your Web application code itself. You should remove any signs of your legacy UI. If you code was well isolated from UI, it will be easier, if not — this work will be closer to development from scratch using legacy source code just for reference. Not to worry — rewriting is very useful. Who could to all the work right from the first attempt?