In the race towards miniaturization in nanoelectronics, magnetic nanoparticles (MNPs) have emerged as potential candidates for their integration in ultrahigh-density recording media. Molecular-based materials open the possibility to design new tailor-made MNPs with variable composition and sizes, which benefit from the intrinsic properties of these materials. Before their implementation in real devices is reached, a precise organization on surfaces and a reliable characterization and manipulation of their individual magnetic behavior are required. In this paper, it is demonstrated how molecular-based MNPs are accurately organized on surfaces and how the magnetic properties of the individual MNPs are detected and tuned by means of low-temperature magnetic force microscopy (LT-MFM) with variable magnetic field. The magnetization reversal on isolated and organized MNPs is investigated; in addition, the temperature dependence of their magnetic response is evaluated.