Hello Brian Bogaert,

You will want to make sure you have copied over any important data first just in case any mistakes are made.
Second you will want to delete the following directories on your secondary disk named D: or eve E: or F:

x:\program files
x:\program files(x86)

You may need to take ownership of the directories before you delete them, you can use this neat tool for quicking assuming control of that data before deleting it.

Alternatively, if you make a copy of the data on the secondary disk to an external backup or even the C:\ you could opt to format the disk then copy your data back over.
Tap or click here to see how to format an existing partition.