Evaporation of a particle laden sessile drop can lead to complex surface patterns with structural hierarchy. Most commonly, the dispersed particles are inert. We have recently reported that when the sessile drop contains reactive ZnO nanoparticles, solidified Bénard-Marangoni (BM) cells with dendritic micromorphology were formed in the residual surface pattern from in situ-generated nanoclusters. Here, we report the effect of substrate chemistry on the residual pattern from the evaporation of nanofluids containing ZnO particles dispersed in a mixture of cyclohexane and isobutylamine, by comparing three different substrates: glass, silicon, and hydrophilized silicon. In particular, we performed a quantitative analysis of the BM cell size, distribution, and the cell morphological characteristics via the fractal dimension analysis. We find that the size dimension λBM of the dendritic Bénard-Marangoni cells varied on the different substrates, attributed to their different hydrophilicity and affinity for water molecules, evident from the different polar components γP in their surface free energy from the Owens-Wendt analysis. The average BM cell size was the smallest for the glass substrate (λBM = 289 μm) and comparable for the unmodified and UV/ozone-treated silicon wafers (with λBM = 466 and 423 μm, respectively). The fractal dimension analysis provided a quantitative description of the BM cells with complex structural hierarchy, highlighting the differences in the geometric features of the surface patterns resulting from different substrate chemistry. We also found that the fractal dimensions depended on the BM cell size, attributing it to two different regimes: the growing fractals and the maturing fractals.