An autofocus apparatus includes, in one embodiment, a light source; a splitter; a fiber optic circulator; an optical collimator; a balance detector; and a microprocessor. The fiber optic circulator couples one of the split light signals at a first port, to the optical collimator at a second port, and to the balance detector at the third port. The optical collimator directs the light beam from the fiber optic circulator onto a sample through a Dichroic mirror and a microscope objective. The balance detector uses another one of the split light signals as an input, and converts a light signal, reflected off of a substrate the sample is placed on, into an analog voltage signal. The microprocessor processes the output of the balance detector and position feedbacks from an adjustable microscopy stage to generate a command for moving the position of the adjustable microscopy stage to achieve a desired focus.