The invention relates to a method and a device for manipulating samples, in particular tissue samples, comprising at least one needle (3) for punching samples out of preparations (5), in particular at defined points on prepared tissue sections and a control device (13) for controlling the needle (3). The aim of the invention is to provide a method and a device, which allow a simple selection of desired punching positions on the preparations (5) and enable a rapid, simple and automatic manipulation of samples. To achieve this, the device is equipped with a camera (14) for capturing images of the surface of the preparations (5), in addition to a unit for superimposing the captured images of the preparations (5) on digital, microscopic images of sections of said preparations (5) that are stored in a memory, a display (12) for reproducing the superimposed images and a unit for applying markings to determine the defined punching positions, said unit being connected to the control device (13).