Interacting with the host OS
I shall answer your second part first.


  is it possible to run native windows code directly from the micro controller


Certainly not, no.  Simply because native Windows code need Windows to run, and needs to be compiled for the host processor - and neither of those can be done on a little Atmel.

The first part of your question:


  is there any premade libraries that does the bulk of the coding work for me?


Almost certainly, yes.  Look on the Atmel site, you will find some.  I personally am not up on Atmel, but all the other manufacturers I can think of provide either full example code, or libraries to incorporate in your own code (such as Microchip's Harmony library), so Atmel certainly will too.