Reformatting the Hard-Disk issue?

I recently did the zero-out erase several times due to issues with the system running smoothly. I expected to come out of the reformat with a clean HD. However, after I partitioned a new space, there were three folders and two files remaining on the disk. I'm afraid that it may be some corrupt files that is preventing OS X from operating efficiently. The files take up a bit over 300MB. Called into Apple care services and talked with a senior advisor, but he doesn't seem to know what the files there may signify... Anybody else seem to have any files and folders left after reformatting their hard drive?
Note: I tried to zero-out erase the partition to remove the files several times after the wipe, but no cigar... Also, tried repartitioning, but the 300MB+ files remained persistently.

Okay. I'm going to spend an hour of my life teaching you something...
I've recently upgraded the hard drive in my 17" MacBook Pro. The original drive is now in an enclosure, but I haven't done anything with its contents yet.
Here is a picture of that drive, below which is a screenshot of the drive as it appears in Disk Utility...
Now I'm going to reformat the drive to demonstrate to you, in spite of your expectations, that what I told you above is true...
First, I'll select the drive in DU (it is called Other World Computing here because that's who makes the enclosure) and choose Erase:
Now, the drive has been erased, its two partitions destroyed, and we see that in the new volume, 425 MB of space have been used for 40 files.
You mentioned something about partitioning your drive (although by your description, it isn't exactly clear what you meant), so I've partitioned my drive in half, and we see that 301.1 MB of space is now being used on the volume Untitled 1. (Take my word, please, that the volume Untitled 2 is using about the same amount of space for the 40 files it also contains.
Now, let's look at what's inside those folders and files using RBrowser. (Apologies in advance for screwing up the formatting of your topic by posting such a large image.):
So, here we are. The folders and files that are created when you format a hard drive are created by the system. It is normal behavior, and behavior you should expect to see when formatting a hard drive anew.
Good luck!

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