Array scanning methods that focus on the far side and devices configured for use in the same are provided. In reading arrays according to the subject methods, an array is placed in a reading position of a scanning device so that the nominal focal plane of the scanning device is present within the array substrate at a predetermined fixed substrate thickness fraction distance from the far-side of the array, and the array is then read by the device. As such, the subject scanner devices of the present invention are configured to hold an array substrate in a reading position of the device in which the device's nominal focal plane is present within the array substrate. The subject methods and devices find use in a variety of different applications, including both genomic and proteomic applications.