To increase sensing potential, silicon nanowires sensor arrays are confined along a nano-fluidic channel for the selective single molecule detection. The differential conductance of silicon nanowires, tuned with source-drain bias voltage, has been previously demonstrated to be highly sensitive to molecular charge. In this work, we have fabricated SiNWs-based FET (field-effect transistor) arrays, which based on the nano-channel diameter, show selectivity to molecular size. Furthermore, the nanochannel can also be selective to ion charge, either by modifying channels surface, or utilizing the electrical double layer effect. By applying electrophoresis principle, we can now investigate ion transport, nanochannels electrical cross section properties, and analyze low concentration samples, of high ionic strength, by eliminating the Debye screening length factor. By using simple electrical and optical measuring methods, we can validate molecule transport control in a 100nm thick channel, and distinguish between opposite-charged and size-varied macromolecules.