I have a xslt which can transform 2 different xml input files. the 2 input files are going to be fed to the xslt separately. My doubt is whether it was possible

Yes of course it's possible. There wouldn't be much point in XSLT if you had to write a different stylesheet for every source document.

Do you mean that a single execution of the stylesheet processes two input files to create a single output? In that case you can read one of the input files using the document() function or you can supply it as a stylesheet parameter.

Michael Kay
http://www.saxonica.com/
Author, XSLT Programmer's Reference and XPath 2.0 Programmer's Reference