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The escalating impact and remarkable progress of nanotechnology have shifted the paradigms of medicine and the healthcare system. Nanosystems have emerged, extensively holding the potential to advance disease diagnosis and treatment specificity. The extraordinary attributes imparted by nano-systems have helped in overcoming the limitations of conventional interventions to an extent and led to targeted therapy, to name one. The role of nanotechnology in diagnosis is another breakthrough in its appellation. This article aims to address the current characterization and sample preparation techniques for the analysis of nanosystems and provide insights into novel methodologies and in situ instrumentation that have eased sampling procedures.