The present study investigates pool boiling heat transfer of Novec 649 on structured copper surfaces. Structures with varying height and spacing, in the range of 400–1200 µm, were machined on the boiling surface using electro-discharge machining (EDM). Pool boiling experiments have been performed to estimate the heat transfer performance of pin-fin structures using Novec 649 as the cooling fluid. The heat transfer coefficient (HTC) and the critical heat flux (CHF) limit of the structured surfaces have been estimated and compared to those of the unstructured ones, both in the horizontal and vertical orientation. In this work, the effects of pin fin heights and spacing, with dimensions similar to the capillary length scale, on the heat transfer coefficient and critical heat flux limit are examined. The experimental results demonstrate that adding pin-fin structures significantly enhances boiling heat transfer. Specifically, the HTC and CHF increases by factors of up to 10 and 2.8, respectively, compared to the smooth surface. This enhancement is primarily driven by the wetted area increase due to the pin-fin structures. The HTC per unit wetted area was found to be independent of geometry during the early stage of nucleate boiling and only exhibited a weak dependence on geometry in the later stages. Notably, the HTC per unit wetted area deteriorates when the pin fin spacing is less than the capillary length scale.