Atomic force microscopy (AFM) is an essential nanoinstrument technique for several applications such as cell biology and nanoelectronics metrology and inspection. The need for statistically significant sample sizes means that data collection can be an extremely lengthy process in AFM. The use of a single AFM instrument is known for its very low speed and not being suitable for scanning large areas, resulting in a very-low-throughput measurement. We address this challenge by parallelizing AFM instruments. The parallelization is achieved by miniaturizing the AFM instrument and operating many of them simultaneously. This instrument has the advantages that each miniaturized AFM can be operated independently and that the advances in the field of AFM, both in terms of speed and imaging modalities, can be implemented more easily. Moreover, a parallel AFM instrument also allows one to measure several physical parameters simultaneously; while one instrument measures nano-scale topography, another instrument can measure mechanical, electrical, or thermal properties, making it a lab-on-an-instrument. In this paper, a proof of principle of such a parallel AFM instrument has been demonstrated by analyzing the topography of large samples such as semiconductor wafers. This nanoinstrument provides new research opportunities in the nanometrology of wafers and nanolithography masks by enabling real die-to-die and wafer-level measurements and in cell biology by measuring the nano-scale properties of a large number of cells.