In one aspect, an apparatus for use in a wellbore formed in a formation is disclosed that in one embodiment includes a device for supplying a hydraulic fluid under pressure to a common hydraulic line, a first pump in hydraulic communication with the common hydraulic line via a first variable fluid control device, a second pump in hydraulic communication with the common hydraulic line via a second variable fluid control device, and at least one controller that controls flow of the hydraulic fluid from the first variable flow control device to the first pump and the flow of the hydraulic fluid from the second variable flow control device to the second pump to independently control the operation of the first pump and the second pump. In another aspect, the first pump is coupled to a first probe for extracting fluid from the formation and the second pump is coupled to a second probe for extracting the fluid from the formation.