The iron-based KxFe2-ySe2 superconductor displays phase separation, leading to the coexisting metallic phase embedded in an antiferromagnetic matrix. The metallic character of the system is believed to arise from a percolative granular network affecting normal as well as superconducting state properties. This network can be manipulated and controlled through thermal treatments. In this study, we have used scanning X-ray micro-fluorescence to visualize morphology of the phase separation and the percolation in KxFe2-ySe2, manipulated by distinct thermal treatments, i.e., fast quenching and slow cooling. We find a differing spatial correlation between Fe and K in differently treated samples, ascribed to different Fe vacancy ordering. We have identified an intermediate phase that acts as an interface between the two phases. The high temperature quenching produces oriented clustered microstructure in which the percolation threshold is lower and hence a more effective network for the transport pathways. Instead, the slow cooling results in larger interfaces around the percolation threshold affecting the superconducting properties of the system. The results provide a quantitative characterization of microstructural morphology of differently grown KxFe2-ySe2 showing potential for the design of electronic devices based on sub-micron scale chemical phase separation, thus opening avenues for further studies of complex heterogeneous structures.