Magnetic nano-clusters in silicon involving iron and cobalt were synthesized using low energy (50 keV) ion implantation technique and post-implantation thermal annealing. Before the irradiation, multiple ion-solid interaction simulations were carried out to estimate optimal ion energy and fluence for each experiment. For high-fluence low-energy irradiation of heavy ions in a relatively lighter substrate, modeling the ion irradiation process using dynamic code SDTrimSP showed better agreement with the experimental results compared to the widely used static simulation code TRIM. A saturation in concentration (~ 48%) profile of the 50 keV Fe or Co implants in Si was seen at a fluence of ~ 2 × 1017 ions/cm2. Further study showed that for structures with a curved surface, particularly for nanowires, better simulation results could be extracted using a code "Iradina" as the curve geometry of the target surface can be directly defined in the input file. The compositional, structural, and magnetic properties were studied using Rutherford backscattering spectrometry, X-ray photoelectron spectroscopy, X-ray diffraction, atom probe tomography, and vibrating sample magnetometry. Irradiation of high-current (~ 2 μA/cm2) 50 keV Fe ions into Si at a fluence of 2 × 1017 ions/cm2 showed the formation of Fe5Si3 nano structures in the near-surface region of the substrate. Post-implantation thermal annealing in vacuum at 500 οC for one hour showed a significant enhancement in structural and magnetic properties. Similar high-current irradiation of 50 keV Co with a fluence of 3.2 × 1016 ions/cm2 into Si substrate showed the formation of superparamagnetic structure even at room temperature in the as-implanted samples. The simulation results for irradiation of Co and Fe on the curved surface were validated by ion irradiation on pre-fabricated Si nano tip followed by atom probe tomography analysis.