A micromachined system for electrical field-flow fractionation of small test fluid samples is provided. The system includes a microchannel device comprising a first substrate having a planar inner surface with an electrode formed thereon. A second substrate having a planar inner surface with an electrode formed thereon is positioned over the first substrate so that the respective electrodes face each other. An insulating intermediate layer is interposed between the first and second substrates. The intermediate layer is patterned to form opposing sidewalls of at least one microchannel, with the electrodes on the substrates defining opposing continuous boundaries along the length of the microchannel. Inlet and outlet ports are formed in one or both substrates for allowing fluid flow into and out of the microchannel. The microchannel device can be fabricated with single or multiple microchannels therein for processing single or multiple test fluids. During operation, a voltage differential is applied to the electrodes in order to induce an electric field across the microchannel. This separates particles of different types present in a fluid injected into the microchannel. The separated particles in the fluid can be collected or further processed as desired.