A new method of rapid detection of pathogens by 3D biomolecular filtering and automated indexing plate measurement has been demonstrated. In this process, a liquid containing pathogens is passed through a 3D biomolecular filter composed of planar arrays of MagnetoElastic (ME) biosensors held by a magnetic field.  This filter captures specific target pathogens (in our demonstration case, Salmonella) in the liquid as it passes over the filter. The experiment will be under different Salmonella concentrations, different flowing rate, different number of ME biosensors and different solution volume. Capture of the pathogens is by specific biomolecular recognition, not size exclusion as with traditional filters. After the entire liquid has passed over the filter, the magnetic field is shut off and the individual biosensors collected and dried.  The biosensors are then placed on an indexing plate consisting of an array of rectangular cavities approximately 10% larger in size than the ME biosensors.  A vibrating table is used to vibrate the ME biosensors into motion until each cavity of the plate is occupied by a single ME biosensor. The biosensors are then measured by sequentially positioning the sensors under a surface scanning detection coil for measurement of the final resonance frequency of the biosensors using an automated translation system. In this manner, a single sensor can be measured in less than 2 seconds with 1000 sensors being measured in less than 30 minutes.