In this work, an experimental heat transfer investigation was carried out to investigate the combined influence of both amorphous carbon (a-C) layer thickness and carbon nanofibers (CNFs) on the convective heat transfer behavior. Synthesis of these carbon nanostructures was achieved using catalytic chemical vapor deposition process on a 50 μm nickel wire at 650 °C. Due to their extremely high thermal conductivity, CNFs are used to augment/modify heat transfer surface. However, the inevitable layer of a-C that occurs during the synthesis of the CNFs layer exhibits low thermal conductivity which may result in insulating the surface. In contrast, the amorphous layer helps in supporting and mechanically stabilizing the CNFs layer attachment to the polycrystalline nickel (Ni270) substrate material. To better understand the influences of these two layers on heat transfer, the growth mechanism of the CNFs layer and the layer of carbon is investigated and growth model is proposed. The combined impact of both a-C and CNFs layers on heat transfer performance is studied on three different samples which were synthesized by varying the deposition period (16 min, 23 min, and 30 min). The microwire samples covered with CNF layers were subjected to a uniform flow from a nozzle. Heat transfer measurement was achieved by a controlled heat dissipation through the microwire to attain a constant temperature during the flow. This measurement technique is adopted from hot wire anemometry calibration method. Maximum heat transfer enhancement of 18% was achieved. This enhancement is mainly attributed to the surface roughness and surface area increase of the samples with moderate CNFs surface area coverage on the sample.