In the model window or in the Project Work Space, right-click on the model and choose "Save as".
The way I have my stuff organized is I have a folder called "Animation" tht sits on my desktop, and within it I have subfolders; one for Models, one for Projects (and within it is a subfolder for each project), one for JPEG images that I may use in future projects/rotoscopes, one for completed movies, one for zip files etc..