Half-circular channels, to be used for gas chromatography, were etched isotropically using a mixture of HF, HNO3 and H2O. Two wafers with half-circular channels were bonded on top of each other to yield channels with a circular cross-section. During etching the so-called `loading effect' was encountered: the etch rate depends on the local structure density. To solve this, extra structures were placed around the channels to create an equal structure density over the wafer and so prevent irregularities in channel width. To eliminate the alignment problems that arise when bonding two wafers with isotropically etched channels together, a method which combines deep trench etching, passivation and isotropic etching was developed to construct channels under the surface of a wafer.