A method of making a microarray apparatus with enhanced feature detectability provides for accurate detection of each feature location, regardless of the quality or quantity of signals from hybridized oligomer test probes. The method comprises separately providing a control probe or stilt and an oligomer test probe at each feature location on the microarray, such that each feature comprises a control probe and a test probe. The control probe comprises a sequence of nucleic acids unique to the control probe. The control probe is labeled with a label that emits a control signal. The oligomer test probe is labeled with a test label that emits a test signal distinguishable from the control signal. When the microarray is hybridized and interrogated, the control signal indicates the location of each and every feature on the array and the test signal indicates the location of hybridized oligomer test probes.