With appropriate processing conditions, nanoscale ferromagnetic particles precipitate from nonmagnetic matrix phase in the Co-Cr and Cr-Fe systems. In these heterogeneous alloys, unique magnetic properties are observed. In order to correlate such magnetic properties with the microstructures, we have employed an atom probe field ion microscope (APFIM) and a three dimensional atom probe (3DAP). In the Co-22Cr thin film sputter-deposited at elevated temperatures (~500 K), both APFIM and 3DAP data convincingly showed that the film was composed of lamellae-like ferromagnetic and paramagnetic phases of approximately 8 nm in thickness. On the other hand, it was shown that the films sputter-deposited at ambient temperature was composed of s-Co single phase without significant compositional heterogeneity. Based on these observations, we conclude that phase separation progresses during the growth of the film on a heated substrate. In the Cr-Fe alloy, large negative MR was observed in the as-quenched alloy at liquid helium temperature. However, the MR behavior changes as the phase decomposition progresses by annealing. The change in the MR behavior observed in this alloy with various heat treatment conditions will be discussed based on the microstructural characterization results by APFIM and 3DAP.