My sister is thinking of applying for the Master's degree here in the US. But, she has a three year's bachelors degree certificate from Nepal.
Do u guys have any suggestions on which universities accept 3 years degree program from foreign countries.
Also how can I apply i-20 for her from here?

It depends upon what kind of 3 years degree your sister has, and what she is planning to study?
From my experience, she may have to take some pre-requisites depending upon the masters program, and school. When I was looking for schools accepting 3 years degree (2007-2008) , I had no luck. I applied as transfer student for Undergraduate studies which was the least possible way to get F1 visa at that time. I know at least 10 friends who did exactly the same.
Bottomline, Its not easy for 3-years degree holders to enroll in Masters program. We all ended upon doing undergraduate studies for mere US degree to join IT consultancy later.
Good luck !

University of Dallas, Irving Texas accepts 3 years degree but you have to do some "bridge" course of about 1 year to have american undergraduate degree.

I do not think 3yr's bachelor acceptable,thing is your application may accepted but they ask to complete course works (may be from general english/math) depends on university and department's HEAD. Its very expensive too. I guess its easy to take master's from TU for some subject eg sociology,education. Get master's trascript and ask to apply for graduate program.