Applying for research funding as an independent researcher? I am a Masters degree holder in Computer Science. Where I live, the most popular way of receiving research grants is from the government. There are two problems with that.

First, You have to be enrolled in a Masters or doctorate degree program at the time of applying for funding.

Secondly, the researcher only gets a small amount of pay from the grant(Like about 2 or 3 percent). About 10 to 15 percent is for research supervisor. And remaining is equipment and other costs.

So is there any way of applying for research funding as an independent researcher? 
I am currently enrolled in a Masters program and am very close to getting a grant for my research. But I would like to continue work as a researcher after completing my Masters and would like to apply for funding independently.
Having only a MSc (and not doing a PhD) it might be hard to get an official research funding (although, there are many different programs and maybe there is one for someone with your status; especially if in some way you are still affiliated with an university of institute).

Sadly, (as Paul Hiemstra pointed out) there no such thing as a scientific freelancer. Science market is very far from an unregulated, free market (and the supply is higher than demands, so it is not a place for freelancer jobs).

However, there are two options which may make sense to you:


doing a part-time PhD, or some PhD where you are not expected to be at the univ. all the time; effectively, it may work for you (though, then it will need to be rather at a low-rank univ.; most likely the most important thing is to find a univ. with no to low teaching load + an advisor who does not care (sic!) or one who understands your situation and is willing to participate in such relationship),
considering crowdfunding - i.e. describing you project on a website and gathering from all interested people (like on Kickstarter); here is a list of sites for crowdfunding in science (then it is not from government).