I'm still waiting for you to describe the likely process or processes identified by Activity Monitor. Until then you cannot even get to Step 1.
I recommend you forget about "cleaning up" memory. It is not necessary to concern yourself with such minutia, despite a plethora of popular "cleaning" apps that seek to convince gullible users of their benefit. Attempting to circumvent OS X's memory management will always lead to performance degradation, as well as the likelihood of accelerated hardware failure. If your Mac's performance begins to degrade for reasons you cannot explain, we can help you to troubleshoot that.
All I can tell you is that El Capitan runs perfectly well in 4 GB RAM, running mostly (though not exclusively) Apple software, with no apparent leaks or degraded performance. I have tried and failed to degrade its performance by simultaneously running literally every app that I have installed. Of course flash memory helps.
Here is a screenshot of AM:

This particular Mac has been up for 10 days:
Last login: Thu Jan 14 10:16:10 on console
Restored session: Mon Jan 11 23:55:05 EST 2016
MacBookAir2:~ john$ man leaks
MacBookAir2:~ john$ w
12:13 up 10 days, 1:57, 2 users, load averages: 1.53 1.45 1.41
USER TTY FROM LOGIN@ IDLE WHAT
john console - 14Jan16 10days -
john s000 - 9:31 - w
MacBookAir2:~ john$
Maybe that will get you pointed in the right direction. Good luck.