We report the pinching of an elongated liquid droplet that is confined in a rectangular microchannel. The droplet pinching is induced by a local variation of the channel topography and can lead to its break-up. The modification of the channel topography is either induced by a reversible local dilation of the channel bottom wall or by a confinement gradient that is irreversibly modelled in the channel. Interestingly, in both cases, a few micrometres contraction of the channel height leads to the pinching of the droplet in the direction of the channel width. If this pinching is such that the droplet is no longer confined at the level of its deformation, i.e. the liquid thread becomes 3D, the droplet splits in two. By minimizing the surface energy of the droplet under the channel confinement gradient, we are able to predict its pinching or its break-up, if any. The dynamic of the droplet deformation is then captured by a semi-analytical model, assuming that most of the viscous dissipation is located in the gutters at the four corners of the channel. Conversely, we show that this kinetic model can be used to extract the average topographic variation of the channel, down to few micrometers, by measuring the droplet pinching dynamics under a classical optical microscope.