Q: Delete Mobile Documents directories

I reinstalled OS X on my mac, but I can't get rid of old folders in ~/Library/Mobile Documents (or iCloud drive). Those are only visible in terminal. I would like to keep it clean on my iCloud Drive, but can't figure out how to delete directories from old applications. If I simply delete everything from this folder, it will appear again in seconds. Is there any way to delete these folders from iCloud drive? For example:

2287T87YW3~com~sis~si~myscans

2BUA8C4S2C~com~agilebits~onepassword

2BUA8C4S2C~com~agilebits~onepassword-ios

356QY8883U~com~melodis~soundhound~free

42BZWU92JZ~com~getairfile~ios~AirFile

4R6749AYRE~com~pixelmatorteam~pixelmator

82J93X7T25~com~apple~mobileiphoto

AP637KM5A4~UBI~088~WW

C5Z3V9M735~com~bitmonstergames~lili

CE7D7D92E2~com~wb~Batman~Brawler2013

E24N8SPR73~com~skyjos~fileexplorerfree

EFSFV3Q6SU~com~barrettj~episodetracker~lite

JFJ4SDLLV4~com~mediocre~smashhit

JZKSZCX743~com~square-enix~bloodmasque~e

MVUUK83754~com~itvshowsapp~itvshows3

SCR5F2GB2S~com~trueaxis~skate

U97HH4RE69~com~vimov~weatherhdliteed

UTDYXA6NM2~com~anuman~HomeDesign3D

XXKJ396S2Y~com~autodesk~SketchBookPro

com~apple~Automator

com~apple~CloudDocs

com~apple~Notes

com~apple~Preview

com~apple~QuickTimePlayerX

com~apple~ScriptEditor2

com~apple~TextEdit

com~apple~mail

com~apple~shoebox

com~apple~system~spotlight