The study focuses on the controlled modification of the surface topography of Ti6Al4V alloy and AISI 304 L stainless steel using pulsating water jet (PWJ) technology. While previous research analyzed these materials separately, this work compares, for the first time, the characteristics of surfaces generated on both materials under identical conditions. Surface modification was carried out using linear and perpendicularly interlaced trajectories at frequencies of fs = 20 kHz and fs = 40 kHz. At fs = 20 kHz, a higher degree of erosion was observed on Ti6Al4V. Conversely, at fs = 40 kHz, the AISI 304 L steel exhibited significantly higher surface roughness Sa, reaching a maximum of Sa = 25.56 μm for the linear trajectory, nearly three times the value (9.17 μm) measured on Ti6Al4V under the same conditions. This phenomenon results from the distinct responses of the materials to cyclic loading, governed by their specific mechanical properties, particularly the ratio of strength, toughness, and plasticity, where Ti alloys are subject to continuous erosion and AISI steels require exceeding a critical load threshold, after which rapid material removal occurs. The results indicate that the material’s ability to absorb impact energy through plastic deformation plays a key role in the formation of surface topography. At the same time, the perpendicular interlaced trajectory can machine the surface more homogeneously and isotropically, which shows its advantage over the linear trajectory. The study, therefore, contributes to a deeper understanding of PWJ interactions with metallic surfaces and provides data to enable the targeted creation of surface structures with defined topographical characteristics.