One of the methods used for fabrication of microelements is ion track lithography, and especially deep proton lithography. Structural depth of the produced elements depends on the energy of the protons. Equally important are the deposited dose and the time of development. One type of element where the thicknesses or depths are important is channels, used in microfluidic setups or used as rectangular waveguides. The waveguides can be obtained both by filling in with a different material and by the change of the refraction index. The shape of the obtained channels is important in both applications. The advantage of deep proton lithography is the possibility of influencing the shape of the channels by controlling the parameters of the radiation process. When using deep proton lithography to fabricate channels, it is necessary to precisely measure the dose deposited inside the material. A new method of channel fabrication, where the deposited dose is measured in the plane before the target, is presented. This is done with the use of a novel deep proton lithography setup operating in air. Experimental results are presented for such a setup built for the tandem accelerator in Erlangen, Germany.