How can I remove all Time Machine data from an external HD, while retaining the other folders/files on the disk?

I recently replaced my old Macbook Pro with a new Macbook Pro Retina.
The original MBP had Time Machine set up on an external HD, and I also had some manually saved/backed up files (stuff that didn't need incremental backups; very old stuff) on the disk as well, in folders. This worked fine and well for the life of the original MBP.
When I set up the MBPr, I did not elect to transfer everything over from a Time Machine disk, as I wanted a Fresh Install; I chose to just re-download/install the apps I needed from the App Store. Much cleaner, more stable. I updated to Yosemite immediately so, it gave me more of a clean install.
The problem is, Time Machine now won't read any Time Machine backups from that disk. Migration assistant can pull data from it, but it's a bit wonky. It was easier to just manually copy over what I needed.
Now, I just want to "reset", and completely remove the old Time Machine data from the external hard drive, since it is completely useless to me now (I can't access it on this computer, and it's taking up space). I want to remove the Time Machine data, as if it were never there, but keep my other folders/files that are on the disk (so, a format is not feasible).
I will then set the disk up as a new, fresh Time Machine disk for the new MBPr.
What is the proper method for removing Time Machine data from an external disk (which doesn't seem to be associated with this machine anyway)? I know a simple rm -rf will cause problems.
Thanks for any help provided.

See the yellow box in #12 of Time Machine - Frequently Asked Questions (or use the link in *User Tips* at the top of this forum).

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How can I remove all Time Machine data from an external HD, while retaining the other folders/files on the disk?

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