Vijay,
I don't believe that this is possible in .NET 1.1. In .NET 2.0, you
will be able to modify the project file so that it can accept conditions
(and you can write your own tasks which will affect the build output through
the MSBUILD engine).
However, I don't know why you would want to do this. Why not just use a
DEFINE statement and have different build configurations based on what you
have defined?
Hope this helps.