MachineKeys folder stores certificate keys that are used by IIS. This folder may fill up with thousands of files in a short time due to a permission or application code related issue.
The permanent solution would be correcting permissions or fixing the code so that the keys in this folder are automatically removed. However, if the permanent fix is taking long time, you may need a practical way of removing old files in the meantime.
Open Command Prompt as Administrator and run the following command to remove files older than 90 days in the MachineKeys folder