Matlab: read multiple files

Like Cris noticed, you have some issues with how you structured your for loop. You are trying to use 'b', and 'c' before they are even given any data (in the second and third times through the loop). Assuming that you have a reason for structuring your program the way you do (I would rewrite the loop so that you do not use 'a','b', or 'c'. And just send 'myfunction' the appropriate index of 'mat') The following should work:

dirMask = '\myfolder\*.wav';  
fileRoot = fileparts(dirMask);
Files=dir(dirMask);

N = natsortfiles({Files.name});
C = cell(size(N));
D = cell(size(N));

a = {};
b = {};
c = {};

for k = 1:numel(N)
    str =fullfile(fileRoot, Files(k).name);
    [C{k},D{k}] = audioread(str);

    mat = [C(:)];
    fs = [D(:)];

    a=mat{1};
    b=mat{2};
    c=mat{3};
end

myfunction(a,Files(1).name);
myfunction(b,Files(2).name);
myfunction(c,Files(3).name);

EDIT

I wanted to take a moment to clarify what I meant by saying that I would not use the a, b, or c variables. Please note that I could be missing something in what you were asking so I might be explaining things you already know.

In a certain scenarios like this it is possible to articulate exactly how many variables you will be using. In your case, you know that you have exactly 3 audio files that you are going to process. So, variables a, b, and c can come out. Great, but what if you have to throw another audio file in? Now you need to go back in and add a 'd' variable and another call to 'myfunction'. There is a better way, that not only reduces complexity but also extends functionality to the program. See the following code:

%same as your code
dirMask = '\myfolder\*.wav';
fileRoot = fileparts(dirMask);
Files = dir(dirMask);

%slight variable name change, k->idx, slightly more meaningful. 
%also removed N, simplifying things a little.
for idx = 1:numel(Files)
    %meaningful variable name change str -> filepath.
    filepath = fullfile(fileRoot, Files(idx).name);

    %It was unclear if you were actually using the Fs component returned
    %from the 'audioread' call. I wanted to make sure that we kept access
    %to that data. Note that we have removed 'mat' and 'fs'. We can hold
    %all of that data inside one variable, 'audio', which simplifies the 
    %program.
    [audio{idx}.('data'), audio{idx}.('rate')] = audioread(filepath);

    %this function call sends exactly the same data that your version did
    %but note that we have to unpack it a little by adding the .('data').
    myfunction(audio{idx}.('data'), Files(idx).name);
end