Should I run the Mac Pro while it is open?

I think that the loud fan noise coming from my Mac Pro is the GPU. It's a loud humming fan noise. I want to try holding the fan down on it while the computer is running to see if it stops making the noise, but I'm afraid to open the Mac while it's running. Is it OK to open it while it's running?
Sorry if this is a stupid question, but this is the first Mac Pro I've used, and I'm afraid that I will break my $1000 computer.

Thanks for the recommendation. Hardware Monitor reported the same temperatures as iStat Menus, but it's more feature-robust. I like that guy's note on how it's not an App Store App
I actually opened my Mac while it was running and held down the GPU fan, and the weird lawnmower noise was coming from it. Some blasting from a compressed air can seemed to fix it, but the main fan is still a bit noisy. I think it's just worn down (since this is a used PC that I bought) and could use some lube.
The hatter wrote:
We have heard and found lately even and over time that Hardware Monitor is most accurate and thorough for monitoring senors readings.
http://www.bresink.com/osx/HardwareMonitor.html

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    I have the 64-bit version of Solidworks running on my Mac Pro and it's a screamer!
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    Alright CT, here's the deal.
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