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 (i.e. not the version included in the official fieldtrip releases). Make sure you use an up to date version available from the vandermeerlab code repository (see also the guide on how to use this).