Instructions
Insert the Controller Pak in one of your controllers and turn on the Nintendo 64 while pressing down and holding the "Start" button on the controller connected to slot number one on your console.
Use your joypad to navigate your way through the Controller Pak menu that appears if the game developers utilized this feature.
Highlight the saves you wish to eliminate and follow the on-screen instructions to delete the selected data. The extra space on the Controller Pak created by this action can now be used to save data relating to other games.