sairam,
I’m afraid there are no in-built features in MyEclipse to compress Javascript files.
Regarding the Google’s Closure Compiler, there is a plugin which helps you compress files using Google’s Closure Compiler. Download the Rockstarapps eclipse plugin zip file from this blog post, extract the downloaded zip file and copy everything, file and subdirectories, to the <MyEclipse installation directory>/dropins directory and restart MyEclipse. Right click on the Javascript/CSS file and you should see the menu Rockstarapps. (I checked it at my end and could compress the Javascript files using Rockstarapps > Compress Javascript context menu).
If this is not what you are looking for, I suggest you to cross post on eclipse forums for better support on this query, as MyEclipse is based on eclipse.
Let us know how it works for you.