A new soft-handed vacuum chuck has been developed to allow the precise measurement of the placement accuracies of X-ray masks and wafers, which are deformed by stresses in processes. As their thicknesses are thin, it is difficult to clamp them without deformation. The chuck has three vacuum pinpads that prevent lateral movement and enable a vacuum seal. This set-up enables a lateral clamping force that can bear an acceleration of 0.3 g and clamping without deformation. Deflections of a 3-inch silicon wafer and an X-ray mask substrate with a 30-mm-square window calculated with the finite element method were minimized at the support radius of 24 mm and 29 mm. Using this chuck with a NIKON 3 I laser interferometry coordinate-measuring machine, we can measure the placement accuracies of an X-ray mask and a reticle with good repeatability at less than 20 nm (3σ).