Q: Is there any way to manually clean up the memory other than a reboot?

If you are referring to memory (as opposed to disk space) then it is normal for OS X to use all of it. Memory that is not used is wasted. It is designed to be used that way to maximize performance.

El Capitan manages your memory. It will use as much as necessary all the time. There is no advantage to having unused memory. The only time to do something is if you are using a lot of swap or the there is a red indicator on your memory status.

In that case there is a program or process leaking memory. That means it is not releasing memory when it should, and is considered a bug that only its developer can fix. Minor memory leaks are not unusual, but not to the extent you describe. Determining which program or process can be challenging.

You can use the command leaks to identify whether a specific process is doing that, but its results can be inconclusive, and you have to know in advance which process you suspect is responsible. Most likely it will be a non-Apple product, though certain Apple software has been known to leak memory in rare circumstances.

To potentially identify likely culprits use Activity Monitor, click the Memory tab, and sort processes by memory. Start by identifying the process with the largest memory value other than kernel_task.

Compressed memory refers to memory that has been compressed using OS X's proprietary compression algorithm. Virtual memory refers to memory contents that have been written to mass storage, which is slower than RAM. If your Mac uses a rotational hard disk drive virtual memory usage will be very slow. Compressed memory is normal and your Mac's performance will not be affected by memory compression. On the other hand if the "memory pressure" graph becomes "red" it's an indication that your Mac is relying upon virtual memory, and its performance will degrade.

What is unused memory used for?

Do you honestly think that compressed memory is as slow as swapping to disk? dream on.

And if you do you can turn it off.

1. Open up Terminal
2. Type in: sysctl vm.compressor_mode
3. (you should see 'vm.compressor_mode: 4' here, which indicates compressed swap is enabled)
4. Type in the following: sudo nvram boot-args=vm_compressor=1
5. reboot
6. After reboot, verify it worked, open up Terminal, and do 'sysctl vm.compressor_mode'. You should see 1 printed.

Then why are you suggesting it?

OS X's memory compression algorithm really will have negligible effect on performance. I have quantified it, and it is essentially zero. You are welcome to do so yourself.

Compression will not occur unless you need more memory than you have. Adding more memory will delay the onset of memory compression. However, it is not a cure for memory leaks. If a process is leaking, it will take all available memory... eventually. If that "eventually" is on the order of weeks or months it's not worth investigating. Rebooting every so often, even if it's in response to an OS X update, is normal.

They are all pretty standard programs.

If to you "pretty standard" means products from Adobe, Google, or Microsoft, anything is possible. None of them have demonstrated any particular aptitude for — or apparent interest in — developing efficient OS X programs. "Anti-virus", "cleaning" products or similarly ill-conceived garbage is even worse. Identify the suspect processes using Activity Monitor as I suggested.

Where do you plan on putting the tasks that would have need compressing for lack of real Ram, disk is slow, what's your plan?

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.