Bilayer magnetic nanostructures are currently of interest in a variety of applications due to the ability to combine complementary properties of each layer. One key area is data storage where extending hard disk drive (HDD) storage density may be achieved by storing each bit of data in an individual magnetic nanostructure. Whilst several magnetometry techniques are capable of measuring the properties of arrays of magnetic nanostructures, very few are sensitive enough to measure an individual magnetic nanostructure. An electrical technique termed anomalous Hall effect (AHE) magnetometry is used in this work due to its high sensitivity. In this technique the structure is fabricated on a Hall cross, and a current is applied and the transverse voltage measured whilst sweeping an external magnetic field. Bilayer magnetic nanostructures formed from separated Co/Pd and Co/Ni multilayers were measured for the first time with this technique, which showed that an asymmetry is seen in their hysteresis loops when the two layers are magnetically decoupled. It is demonstrated that this is due to a combination of a very small giant magnetoresistance (GMR) effect present in the magnetic nanostructure, and the Hall cross offset voltage which results from small imperfections in the shape of the cross. A finite element simulation is used to provide quantitative evidence for this model. These results indicate that asymmetry will be seen in Hall measurements of other materials which exhibit magnetoresistance. Bilayers of FePt and FeRh were also investigated as these materials are of interest for a future HDD system where the structure is heated, and the FeRh undergoes a ferromagnetic transition causing it to assist the switching of the FePt. These thin films are difficult to deposit whilst achieving chemical ordering in both layers. FeRh/FePt films are deposited, before greater ordering is demonstrated with an FePt/FeRh film. It is demonstrated that AHE magnetometry can provide a similar level of measurement information of bilayer nanostructures of these materials as bulk magnetometry techniques can provide of the thin film.