I've been modifying waterfalls for my water mod and had to delete many of the vanilla waterfalls. To my surprise it appears every waterfall I've delete is bunched up together at the center of the map:

http://cloud.steampowered.com/ugc/504638771990540697/93812E6D9C8CA11D6DB98AB3F8F5145C0B740937/

Any ideas on how to fix this? I apologize if this has been covered already but I couldn't find any information on it.

"Deleting" Skyrim.ESM placed stuff is probably a bad idea. In previous games, doing so could cause CTD's. Instead, set PlayerREF in (any) cell as the enable parent of stuff you want gone, then tick the "Set enable state to opposite of parent" flag in the REFRs' "Enable Parent" tabs and set their coordinates to -30,000 or so that you'll not have to see them in the render window. This is how FO3Edit/TES4Edit undeletes, safely removing Beth placed stuff. Incidentally, it will also fix your problem.

What do you mean by set PlayerREF? Sorry I'm a bit of a newb at this. Also is there an easy way to see what objects I have already set to delete in the CK?

In any placed item's edit window, the "Enable Parent" tab lets you choose an enable parent. PlayerREF is the special reference that is the player, ACHR 00000014, found in the (any) cell of the Enable Parent tab's window when selecting. To see what you've "deleted", open your plugin with the CK, then go to Data > Details, select your plugin and sort by deletion. Multiselect all deleted forms (write down their FormIDs) and hit the delete key which will mark the overrides as "Ignored", flagging them for removal next save. You can then go back, after closing/reopening the CK, and remove the REFs with the enable parentage method.

Thanks so much. I really appreciate it. Lot of work to do since I've deleted so many of waterfalls.

No problem and I hope all goes well. Make sure to double check, after setting up enable parentage/coordinates, that the the edits stuck.

For whatever it's worth, confirming the same thing. There's a couple of nice big chunks of rock and trees from stuff I deleted sitting up there now. Oddly though, only from Markarth. Nothing I deleted in Riften or at the farmhouse in my alt-start mod.

Is hiding them underground and scaling them small an option?

That's what the guy's have advised in this thread. Shouldn't be a need to scale. Just set their z values uber low, and set them to be the opposite of the player enable state.

How is this method different from just checking the "initially disabled" box on everything you want to remove?

Because disabled/enabled states can persist in save games. Parent relations do not.

That's very good to know, thank you!