Methods and systems for measuring variations in head-disk clearance in a hard disk drive. User generated data is randomly selected at a controller of the hard disk drive wherein the user generated data is stored on a disk associated with the hard disk drive. A reference point associated with the user generated data is stored on a storage medium associated with the hard disk drive. The user generated data is read at the controller. The user generated data is analyzed with the reference point using more than two frequencies, at the controller, to obtain a variation in measurement of the head-disk clearance.