A clean tool uninstall has two parts.
Every ModelTools tool uses the Windows operating system registry.
Every tool has a panel which shows the regsitry's entries and, important here, gives you the opportunity to remove those entries.
Before deleting a tool's executable code, run the tool one last time. Go to Setup | Registry (shown below for ModelSolver).
Check Delete application registry on program exit at the bottom of the panel. Exit the tool. The tool's registry entries are now totally cleaned up. Now delete the tool's executable code.