To load *.Ncs (Neuralynx Continuously Sampled, sometimes also referred to as CSC for Continuously Sampled Channel) files in MATLAB, use the following:

fc = FindFiles('*.ncs');
data = ft_read_neuralynx_interp(fc);

This will create a fieldtrip data structure with all CSCs, filling any gaps in the original data with NaNs.

Note that ft_read_neuralynx_interp calls a custom version of ft_read_data. Make sure you use the version available from the vandermeerlab code repository (see also the guide on how to use this).