mac pro 6,1 2013: can you take the cover off for cooling? Cooling Options?

I've installed an external fan, like a real fan, not a computer one, also installed a laptop aluminum cooler in the bot and it cooled from 55 to 45, I'm starting to search for a liquid laptop cooler so and maybe try with that...

Removing the case ruins the ability of the fan to move air past the central cooling core. It is a completely Bad Idea. This model of the Mac Pro is all about running big hot processors, lots of RAM memory, and multiple high-end graphics cards, and powering and cooling all of them adequately. All the Mac Pro models, but especially the 6,1 model adjust the fan speed based on measured temperatures at several different places inside the computer.

Do make sure the air inlets at the bottom are unobstructed.

if internal temperatures get too high (but long before it suffers internal damage) your Mac Pro will do an emergency, uncontrolled power off to protect itself. If you think it may not be cooling properly, you should run the diagnostic to make certain all the internal sensors are working correctly.

Taking off the cover probably isn't a good idea given the cooling system design. The cover is also part of the cooling system. Perhaps some external cooling such as a fan would work.

In addition to the other comments, and I would also confirm do not try running it with the cover off, the case is intended to get hot as this is part of the means by which heat is transferred away from the internal components.

The Mac is fitted with various internal heat sensors and as Grant says, it will auto power down if it feels one of these is indicating an excessive temperature.

It will not really apply to the current Mac Pro, but a standard (Windows) desktop PC is designed to be upgradeable by the owner. It is possible to upgrade such a PC to a level that it would exceed the original design specifications, for example either by fitting a very powerful video card or more powerful CPU chips. In the case of such a PC it is therefore sometimes necessary to fit more powerful cooling fans than it originally came with, or even go to the level of using liquid cooling systems. However the current Mac Pro does not let you upgrade the CPU or video card so you cannot realistically 'upgrade' it to a level that would exceed the original Apple design specifications and therefore the original fan should be sufficient.

Apple do a lot of testing of their designs and in general they are extremely reliable because Apple are very conservative with their specifications.

I would install fan speed and temperature monitor app to see what is going one. Maybe problems with fan. I use Macs Fan Control.

http://www.crystalidea.com/macs-fan-control

I would also make sure the the ventilation intake at the bottom of the cylinder are clean. My tend to collect dust/hair (I have cats) which obstructs air flow