In this work, we describe an approach to determine the distance separating a magnetic address from a scanning magnetoresistive sensor – a critical adjustable parameter for certain bioassay analyses where magnetic nanoparticles are used as labels. Our approach is leveraged from the harmonic ratio method (HRM), a method used in the hard drive industry to control the distance separating a magnetoresistive read head from its data platter with nanometer resolution. At the heart of the HRM is an amplitude comparison of a signal’s fundamental frequency to that of its harmonics. When the signal is derived from the magnetic field pattern of a periodic array of magnetic addresses, the harmonic ratio contains the information necessary to determine the separation between the address array and the read head. The elegance of the HRM is that there is no need of additional components to the detection platform to determine a separation distance; the streaming “bit signal” contains all the information needed. In this work we demonstrate that the tenets governing HRM used in the hard drive industry can be applied to the bioanalytical arena where submicron to 100 μm separations are required.