An experimental approach has been used to investigate the influence of a thin layer of carbon nanotubes (CNTs) on the convective heat transfer performance under impinging flow conditions. A successful synthesis of CNT layers was achieved using a thermal catalytic vapor deposition process (TCVD) on silicon sample substrates. Three different structural arrangements, with fully covered, inline, and staggered patterned layers of CNTs, were used to evaluate their heat transfer potential. Systematic surface characterizations were made using scanning electron microscope (SEM) and confocal microscopy. The external surface area ratio of fully covered, staggered, and inline arrangement was obtained to be 4.57, 2.80, and 2.89, respectively. The surface roughness of the fully covered, staggered, and inline arrangement was measured to be (Sa = 0.365 μm, Sq = 0.48 μm), (Sa = 0.969 μm, Sq = 1.291 μm), and (Sa = 1.668 μm, Sq = 1.957 μm), respectively. On average, heat transfer enhancements of 1.4% and − 2.1% were obtained for staggered and inline arrangement of the CNTs layer. This is attributed to the negligible improvement on the effective thermal resistance due to the small area coverage of the CNT layer. In contrast, the fully covered samples enhanced the heat transfer up to 20%. The deposited CNT layer plays a significant role in reducing the effective thermal resistance of the sample, which contributes to the enhancement of heat transfer.