An imaging reader includes a light source generating an illumination beam over a working distance, and a variable focus imaging assembly with an image sensor, a variable focus optical element, a variable focus imaging controller that controls operation of the variable focus optical element to define a plurality of imaging planes over the working distance. The variable focus imaging controller assesses a variety of scanning parameters and determines the number of imaging planes over the working distance and the distance of each of imaging plane from the image sensor, to allow the imaging reader to capture images of a target object only at each of the imaging planes, thereby avoiding time-consuming autofocusing on the target. The imaging reader captures images in a sequential order greatly reducing image capture and image analysis processing time.