You need to interpolate them to the same size using interp1.
clc
clear
close all
[index, sname] = textscan('filenr.lis','%d %s');
N = length(index) ;
iwant = cell(N,1) ;
for k = 1:N
wavfilepath = '\\GSE\\';
sfiles =char(sname(k,:));
s = [wavfilepath sfiles];
fid = fopen(s);
[data] = readfile(fid);
iwant{k} = data{1}; % load data of the file
end
% do interpolatio to make them to same size
L = cellfun(@length,iwant) ; % length of each array
Lmax = max(L) ;
data = zeros(L,N) ;
for i = 1:N
x = 1:length(iwant{i}) ;
y = iwant{i} ;
xi = linspace(1,length(iwant{i}),Lmax) ;
data(:,i) = interp1(x',y,xi') ;
end
