We present a simple experimental method for determination of limiting intrinsic fixed-pattern non-uniformity (NU) due to fabrication process in two-dimensional CCD multiplexers (MUXs) that are used for hybrid focal plane arrays. Here, this is done by determining separately the two NUs viz. that are $V_T$ dependent and $V_T$ independent. From these measurements, process dependent NU can be extracted. It is argued that $V_T$ dependent NU can be eliminated by designing novel input circuits whereas $V_T$ independent NU, primarily, dependent on process control and material variations may be reduced but cannot be eliminated completely and hence limits the FPA performance eventually.