My recommendation is to keep the original files and also the mastered sounds in separated folders. I have a folder of raw recordings and also the respective folders on my personal library.
When I copy my recordings from the recorder's memory, I first rename all the files, then make a backup and work over the originals. Normally I first mix the channels if it's needed, then remove unwanted sounds, cut/add silences, fades, etc. All the commmon editing stuff. Then I use some EQ if it's needed, or noise reduction, depending on the sound. EQ can do a lot of corrective things if you know how to use it correctly.
You have to be careful with Noise Reduction. From my experience, it's better to start using some EQ, notch filtering, etc. If there's more specific noise, it's good to try with some noise reduction (mostly RX and Z-Noise in my case).
And the levels... For me it depends on the sound that is going to be mastered. The first recommendation I would give is to record with the final levels in mind, so you don't have to worry too much about it when mastering your recordings. Obviously it depends of the circumstances and the sounds recorded. Some sounds are fine on it's recording level, with other kind I try to get -0.5dB peaks, etc.
In this final step of mastering, expanders/limiters such as L2 or multi-band tools such as Waves C4 or McDSP ML400 are really great. That kind of tools are pretty versatile, both for noise reduction and expanding/limiting tasks. Of course it depends on whatever fits better for you and what exactly do you need. That's because is useful to keep the raw files, in case you want to go back and re-edit the files.
For me the main goal of mastering sfx is to get clean sounds. Just that, everything else such as adding puch, warmth, etc it's more for an editing/design process.