Abstract Machining of cooling holes on thermal barrier coated superalloy components using a nanosecond (ns) laser generates considerable collateral damage such as recast layer, spatter and delamination of the ceramic coating. However, recent studies have suggested that these damages can be virtually eliminated by machining with femtosecond (fs) lasers. A detailed study on the microstructural characteristics of fs laser machined holes with diameters of 300 μm and 600 μm, generated on thermal barrier coated superalloy CMSX4 under various processing conditions has been conducted. Features examined include the shape, size and the surface finish of the hole wall. Femtosecond laser machined holes with a surface roughness of less than 2 μm and no major collateral damage could be generated in coated samples up to a thickness of 1.5 mm. The machining was found to cause minor ablative material removal from the top ceramic layer within 100 μm of the outer edge of the hole. The presence of machined holes did not affect the thermal cycling life at 1100 °C of the coated samples.