When I ctrl+shift+f up the project code, its doing its job just fine, everywhere.
But its messing the CSS, specially those filter parts and adding bunch of spaces.
Also how do I specify some portion of Java code to not be formated by that command ?
To prevent specific portions of Java code from being formatted, go to "Window > Preferences > Java > Code Style > Formatter". Click the "Edit..." button, go to the "Off/On Tags" tab and enable the tags. Afterwards, you can simply embed those tags in Java code to disable the formatting in-between them. If you don't change the default tags, something like this will do :
//@formatter:off
this.
portion.of(code
); // will not be touched by the formatter
//@formatter:on
but this will be
reformatted.
IIRC, this option only exists since Eclipse 3.6.
As for css code, if you have installed Eclipse WTP, go to "Window > Preferences > Web > CSS Files > Editor" and you will find some basic formatting options there.