A method of separating a liquid droplet from a liquid portion in a biological sample processing system comprising a liquid droplet manipulation instrument comprising: • at least one electrode array with electrodes for inducing a movement of at least one of a liquid droplet that covers a single electrode and a liquid portion of a larger volume that covers more than one electrode of the electrode array by electrowetting; • a substrate supporting the at least one electrode array; • a control unit capable to define a path for a guided movement of the liquid droplets and liquid portions; • at least one voltage control; • at least one electrode selector connected with the at least one voltage control for individually selecting each electrode of the at least one electrode array and for providing the selected electrode with an individual voltage pulse which is selected from a group comprising a drive voltage, a ground voltage, and a stop voltage; • a central processing unit for controlling the electrode selector and the voltage control; • a container having a top side and a base side with protrusions distributed on the base side; and • a flat polymer film having a lower surface and a hydrophobic upper surface, which is kept at a distance (d) to the base side of the container by the protrusions, the distance (d) defining at least one gap when the container is positioned on the flat polymer film, abutting the latter with its protrusions; wherein the method comprises the steps of: (a) reversibly attaching the container and the flat polymer film to the liquid droplet manipulation instrument so that the lower surface of the flat polymer film is abutting the at least one electrode array; (b) placing in the gap a liquid portion on the hydrophobic upper surface of the flat polymer film and above the at least one electrode array; (c) providing a drive voltage pulse to at least one initial drive electrode along a defined electrode path, thus moving the liquid portion of a larger volume in a first direction; (d) providing at least one of the initial drive electrodes with a ground or stop voltage pulse; and (e) providing a drive voltage pulse to a group of two or more drive electrodes of the electrode array in order to move said liquid portion of a larger volume in a second direction inverse to the first direction. • at least one electrode array with electrodes for inducing a movement of at least one of a liquid droplet that covers a single electrode and a liquid portion of a larger volume that covers more than one electrode of the electrode array by electrowetting; • a substrate supporting the at least one electrode array; • a control unit capable to define a path for a guided movement of the liquid droplets and liquid portions; • at least one voltage control; • at least one electrode selector connected with the at least one voltage control for individually selecting each electrode of the at least one electrode array and for providing the selected electrode with an individual voltage pulse which is selected from a group comprising a drive voltage, a ground voltage, and a stop voltage; • a central processing unit for controlling the electrode selector and the voltage control; • a container having a top side and a base side with protrusions distributed on the base side; and • a flat polymer film having a lower surface and a hydrophobic upper surface, which is kept at a distance (d) to the base side of the container by the protrusions, the distance (d) defining at least one gap when the container is positioned on the flat polymer film, abutting the latter with its protrusions; (a) reversibly attaching the container and the flat polymer film to the liquid droplet manipulation instrument so that the lower surface of the flat polymer film is abutting the at least one electrode array; (b) placing in the gap a liquid portion on the hydrophobic upper surface of the flat polymer film and above the at least one electrode array; (c) providing a drive voltage pulse to at least one initial drive electrode along a defined electrode path, thus moving the liquid portion of a larger volume in a first direction; (d) providing at least one of the initial drive electrodes with a ground or stop voltage pulse; and (e) providing a drive voltage pulse to a group of two or more drive electrodes of the electrode array in order to move said liquid portion of a larger volume in a second direction inverse to the first direction.