We previously developed a simple surface modification procedure to form a nanostructure on a microcapillary surfaces. However, only one set of conditions was examined and further optimization appeared necessary. This paper presents a detailed examination of the surface modification procedure and the effects of the surface modification level on the immobilisation of lipase. We first performed the reaction using a microcapillary with a 320 μm i.d and a 20 cm length. The number of surface amino groups was increased by increasing the content of 3-aminopropyltriethoxysilane in the silylating reagent by 60%, but a much higher content did not further increase the number of amino groups on the surface. The number of immobilised amino groups did not influence the amount of immobilised lipase. The performance of the microcapillary reactors was evaluated using the 7-acetoxycoumarin hydrolysis reaction. The microcapillary reactors showed equal reaction efficiency to each other, implying that surface structure, rather than the number of amino groups, affect microreactor performance. In a comparison of efficiency with a batchwise system, microreactors showed higher efficiency. We also applied our surface modification method to a ceramic microreaction device, which has a square channel (400 μm × 400 μm × 20 cm). The resulting lipase-immobilized ceramic microreaction device retained the same reaction efficiency. These results demonstrate that this modification method is applicable for the further development of microreaction devices.