As a consequence of rapid development of additive manufacturing (3D printing) methods, the academic/industrial demand has been continuously increasing. One field of application is the manufacturing of heat exchanging devices using this promising method. In this regard, understanding the underlying mechanisms from a thermo-hydraulic viewpoint becomes important. Therefore, in this study, scale-resolving large eddy simulation (LES) is applied to reveal the flow details in combination with a model of roughness topology occurring in additive manufacturing. To process the transient LES results, proper orthogonal decomposition (POD) is used to extract the coherent flow structures, and the extended POD is used to rank the flow modes based on thermal importance. The main aim of the present work is to go beyond the conventionally applied methodologies used for the evaluation of surface roughness, i.e., averaged numerical study or experimental overall performance evaluation of the flow/thermal response of additively manufactured surfaces in heat exchangers. This is necessary to reveal the underlying flow mechanisms hidden in the conventional studies. In this study, the behavior of the flow over the micro-scale surface roughness model and its effects on heat transfer are studied by assuming cone-shaped roughness elements with regular placement as the dominant surface roughness structures. The major discussions reveal the footprint of flow mechanisms on the heat transfer coefficient spatial modes on the rough surface. Moreover, comparative study on the flow/thermal behavior at different levels of roughness heights shows the key role of the height-to-base-diameter ratio of the roughness elements in thermal performance.