In recent years, polymers have been popular in industrial applications due to their lightweight, corrosion‐resistant, improved surface polish, ease of manufacturing, cost‐effectiveness, and so forth. Similarly, micro/nano‐indentation has gained popularity as a technique for assessing the surface mechanical characteristics of polymers. The present study conducted comprehensive experiments using cyclic micro‐indentation on engineering polymers, specifically poly‐ether‐ether‐ketone (PEEK), poly(methyl methacrylate) (PMMA), and poly(tetra‐fluoroethylene) (PTFE). An appropriate and optimal indentation method has been proposed after analyzing the behavior and significance of all the input parameters in evaluating the properties. Both constant load multi‐cycle (CLMC) and progressive load multi‐cycle (PLMC) were considered for this investigation. A comparative evaluation has been conducted to assess two multi‐cycle tests on these materials. From the analysis of the input parameters, including maximum loads, loading and unloading rates, and the number of cycles, the unloading rate and indentation cycle are crucial factors in determining hardness (H) and elastic modulus (E). Increasing the loading rates leads to an increase in H and a reduction in E for all three materials. This effect arises from the thermal effect, which is characterized by the creep modulus and a closed hysteresis loop. Employing the holding duration and multiple cycle data in constant load multi‐cycle can significantly influence the creep behavior and use of the hysteresis loop for fatigue behavior. Similarly, a progressive load multi‐cycle indentation with a force greater than 0.5 N and a minimum of five cycles is the most accurate approach for evaluating surface mechanical parameters.