This should be possible in Device Manager.

Open the System control panel by pressing <kbd>Windows</kbd> + <kbd>Break</kbd>, and click on the Device Manager tab. 

[![Screenshot of the Windows ME Device Manager][1]][1]

Expand the 'Floppy disk controllers' and you should see an entry for 'Standard Floppy Disk Controller'. Double-click it and a property sheet will open. 

[![Screenshot of the Windows ME Standard FDC property page][2]][2]

Tick 'Disable in this hardware profile', then 'OK'.


  [1]: https://i.sstatic.net/WEDpb.png
  [2]: https://i.sstatic.net/VAMVI.png