This article describes the CXrL aligner, an experimental x‐ray proximity lithography system developed at the University of Wisconsin Center for X‐Ray Lithography. The main features of the aligner are (1) exposure in an atmospheric He environment; (2) mask to wafer alignment error detection and correction during exposure; and (3) mask to wafer continuous gap setting based on capacitance gauges. The aligner consists of a three‐axes two‐state alignment system for continuous alignment error detection and a piezobased precision mechanical stage for alignment error correction. The wafer is held by a flat vacuum chuck and the mask is held by three vacuum suction cups located around the glass ring. Since the optical system is located outside of the synchrotron radiation path, alignment can be performed during the exposure. We have obtained a noise equivalent misalignment of 2 nm with an alignment signal response time less than 10 ms. An alignment signal repeatability (3σ) better than 0.06 μm has been achieved. In the preliminary evaluation of x‐ray printed patterns, we obtained an overlay accuracy of 0.18 μm, to which the measurement error contributes most.