You could use the function textscan, which lets you select the headerlines to ignore (so you don't need to delete any lines by hand), and also define the number of rows that should be read into MATLAB. EDIT to match newly uploaded textfile.
This code reads that text file, including the header, the matrix, and the trailing data. It also adjusts automatically to the number of columns.
fid = fopen('myexamplefile.txt','rt');
line1 = fgetl(fid);
hdr = regexp(fgetl(fid),'\S+','match');
fmt = repmat('%f',1,numel(hdr));
C = textscan(fid,fmt);
D = textscan(fid,'%s%s%s%s',1,'HeaderLines',1);
fgetl(fid);
E = textscan(fid,'%s%f%f%f%f',1,'HeaderLines',1);
fclose(fid);
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