How will a "local" master's in CSE look when I apply for a Graduate funding in the USA?
PhD positions in universities are limited and given to outstanding students who have a potential for research. If your aim is to pursue your PhD in USA/Germany/Canada etc., I'd highly suggest applying for a Master's in those countries UNLESS your local university is well-known, with good professors and coursework. Your application will be evaluated on:


Your GPA &amp; Test scores
Reputation of university you're graduating from (Master's, undergrad) // And as Daisetsu says, the researchers you work with 
Research aptitude
Reputation of the journals you're published in
Your statement of purpose
Letters of recommendation
Previous work experience


Also ask yourself, "Why a PhD?" What is your career trajectory and will a PhD help you? What about an MBA? How many years can you invest in this? 

To be honest, no one here can tell you your chances of getting into a University for a PhD apart from the admissions committee itself. Spend some more time reading up the requirements of the colleges you're keen on and then arrive at a well informed decision.

Best of luck!