I managed to get it to work by using only the textscan function. I had seen an example using fgetl and I thought I needed it for this application, but it turns out I didn't.
fid=fopen('n90deg'); % Open file
c=1; % Initialize counter
while ~feof(fid); % Run until end of file
tmp=textscan(fid,'%f%f%f%f','Headerlines',2); % Omit first two lines every
% time
n90deg(c,:)=tmp{4}'; % Store the last cell as a row in new matrix
c=c+1; % Add to counter and repeat above steps
end
fclose(fid);
Hopefully someone else will find this useful.