This review provides a comprehensive overview of recent advances in atomic-scale manipulation of two-dimensional (2D) materials, particularly graphene and transition metal dichalcogenides (TMDs), using scanning tunneling microscopy (STM). STM, originally developed for high-resolution imaging, has evolved into a powerful tool for precise manipulation of 2D materials, enabling translational, rotational, folding, picking, and etching operations at the nanoscale. These manipulation techniques are critical for constructing custom heterostructures, tuning electronic properties, and exploring dynamic behaviors such as superlubricity, strain engineering, phase transitions, and quantum confinement effects. We detail the fundamental mechanisms behind STM-based manipulations and present representative experimental results, including stress-induced bandgap modulation, tip-induced phase transformations, and atomic-precision nanostructuring. The versatility and cleanliness of STM offer unique advantages over conventional transfer methods, paving the way for innovative applications in nanoelectronics, quantum devices, and 2D material-based systems. Finally, we discuss current challenges and future prospects of integrating STM manipulation with advanced computational techniques for automated nanofabrication.