A method for determining selected properties of a microplate (130, 200) comprising a plurality of sample wells (220, 222, 224), each sample well being open at a top portion of the microplate and including a well surface (202, 204), the well surface being disposed on the top portion opposite a plate bottom of the microplate, the method comprising: moving the microplate (130, 200) to position an initial x-y position on the microplate in an optical path generated by a laser; positioning an objective lens substantially centered in the optical path in a z-direction to an initial z-position; performing a focusing function to determine a well surface (202, 204) z-position for a current x-y position based on an intensity indicative of a best focus of the well surface; performing the focusing function to determine a plate bottom z-position for the current x-y position based on an intensity indicative of a best focus of the plate bottom; moving the microplate (130, 200) to position a plurality of x-y positions within a selected area of the microplate in the optical path where the selected area encompasses a well bottom of one of the wells (220, 222, 224) on the microplate (130, 200); at each of the plurality of x-y positions, determining the well surface (202, 204) z-position and the plate bottom z-position corresponding to each of the plurality of x-y positions by repeating the steps of positioning the objective lens, performing the focusing function to determine the well surface z-position, and performing the focusing function for the plate bottom z-position; and using the well surface (202, 204) z-positions and the plate bottom z-positions at the plurality of x-y positions to: generate an image in a 3-D format to depict the well bottom and plate bottom; and display the image on a display to illustrate a flatness of the well bottom, the flatness of the well bottom being one of the selected properties of the microplate (130, 200). moving the microplate (130, 200) to position an initial x-y position on the microplate in an optical path generated by a laser; positioning an objective lens substantially centered in the optical path in a z-direction to an initial z-position; performing a focusing function to determine a well surface (202, 204) z-position for a current x-y position based on an intensity indicative of a best focus of the well surface; performing the focusing function to determine a plate bottom z-position for the current x-y position based on an intensity indicative of a best focus of the plate bottom; moving the microplate (130, 200) to position a plurality of x-y positions within a selected area of the microplate in the optical path where the selected area encompasses a well bottom of one of the wells (220, 222, 224) on the microplate (130, 200); at each of the plurality of x-y positions, determining the well surface (202, 204) z-position and the plate bottom z-position corresponding to each of the plurality of x-y positions by repeating the steps of positioning the objective lens, performing the focusing function to determine the well surface z-position, and performing the focusing function for the plate bottom z-position; and using the well surface (202, 204) z-positions and the plate bottom z-positions at the plurality of x-y positions to: generate an image in a 3-D format to depict the well bottom and plate bottom; and display the image on a display to illustrate a flatness of the well bottom, the flatness of the well bottom being one of the selected properties of the microplate (130, 200). generate an image in a 3-D format to depict the well bottom and plate bottom; and display the image on a display to illustrate a flatness of the well bottom, the flatness of the well bottom being one of the selected properties of the microplate (130, 200).