I want to store the all values in a single file. I have 5 data files those files are run at a time and i want to store the all data files output files stored in single file. here i am attached input and corresponding matlab functions.

clear all;
close all;
clc;

count_file = 1;
f1=fopen('input.dat','r'); %%%%%insert input file names in the input.txt
warning on;
while (feof(f1)~=1)
    fname=fgetl(f1); %%%%%%reading the file name inside the input.txt
    fn=fname(1:length(fname)-4);
    fprintf('Processing file:::: %s\n',fname);
    fout=fopen(sprintf('SKU_Backscatter_Coefficient_%s.dat',fn(32:41)),'a');
% % %     fout_hr=fopen(sprintf('SKU_Flux_Var_hr_%sT.dat',fn(1:4)),'a');
% % %     fname=fopen(fname,'r');

% % % fname = 'CAL_LID_L2_05kmAPro-Prov-V3-30.2014-04-26T07-56-49ZD_Subset.hdf';

metadata = hdfread(fname, '/metadata', 'Fields', 'Lidar_Data_Altitudes', 'FirstRecord',1 ,'NumRecords',1);
alts = metadata{1};
numberAlts = length(alts);

latMin = 12;
latMax = 16;

product_name = 'Latitude';
[info, lat] = readHDF(fname,product_name,[0 1],[-9 1]);

latRangeWanted = lat > latMin & lat < latMax;
firstProfile = find(latRangeWanted,1,'first');
lastProfile = find(latRangeWanted,1,'last');

numberProfiles = lastProfile - firstProfile + 1;

product_name = 'Total_Backscatter_Coefficient_532';
[info, sigma] = readHDF(fname,product_name,[firstProfile-1 0],[numberProfiles -9]);

product_name = 'Total_Backscatter_Coefficient_Uncertainty_532';
[info, sigma_uncer] = readHDF(fname,product_name,[firstProfile-1 0],[numberProfiles -9]);

sigma = sigma';
sigma_uncer = sigma_uncer';

product_name = 'Extinction_QC_Flag_532';
[info, extQC] = readHDF(fname,product_name,[firstProfile-1 0 0],[numberProfiles -9 -9]);    

product_name = 'CAD_Score';
[info, CAD] = readHDF(fname,product_name,[firstProfile-1 0 0],[numberProfiles -9 -9]);     

product_name = 'Atmospheric_Volume_Description';
[info, AVD] = readHDF(fname,product_name,[firstProfile-1 0 0],[numberProfiles -9 -9]);    

useSamples = true(numberAlts,numberProfiles);

useSamples(sigma == -9999) = false;

[ftype, subtype] = get_feature_type_and_subtype(AVD);

isAerosol = squeeze(ftype(1,:,:) == 3 | ftype(2,:,:) == 3);
useSamples(~isAerosol) = false;

CAD_fill = -127;
CAD(CAD > 0) = CAD_fill;
goodCAD = squeeze( (CAD(1,:,:) < -20 | CAD(1,:,:) == CAD_fill) &...
                   (CAD(2,:,:) < -20 | CAD(2,:,:) == CAD_fill) );
useSamples(~goodCAD) = false;

extQCfill = 32768;
extQC(ftype ~= 3) = extQCfill;
goodExtQC = squeeze(...
    (extQC(1,:,:) == 0 | extQC(1,:,:) == 1 | extQC(1,:,:) == extQCfill) & ...
    (extQC(2,:,:) == 0 | extQC(2,:,:) == 1 | extQC(2,:,:) == extQCfill)); 
useSamples(~goodExtQC) = false;

useSamples(sigma_uncer > 99.9) = false;

meanSigmaUnscreened = zeros(numberAlts,1);
meanSigmaUnscreened_uncer = zeros(numberAlts,1);
numSamplesUnscreened = zeros(numberAlts,1);
meanSigmaScreened = zeros(numberAlts,1);
meanSigmaScreened_uncer = zeros(numberAlts,1);
numSamplesScreened = zeros(numberAlts,1);

for k = 1:numberAlts

      t = sigma(k,:) ~= -9999;
      meanSigmaUnscreened(k) = mean(sigma(k,t));
      meanSigmaScreened(k) = mean(sigma(k,useSamples(k,:)));
    numSamplesUnscreened(k) = sum(t);
      if numSamplesUnscreened(k) > 0
          meanSigmaUnscreened_uncer(k) = sqrt(sum(sigma_uncer(k,t).^2)./numSamplesUnscreened(k));
      end
      numSamplesScreened(k) = sum(useSamples(k,:));
      if numSamplesScreened(k) > 0
          meanSigmaScreened_uncer(k) = sqrt(sum(sigma_uncer(k,useSamples(k,:)).^2)./numSamplesScreened(k));
      end
  end

   fprintf(fout,'%.3f\n',meanSigmaScreened(count_file,1)); 
   count_file = count_file+1;
   clear meanSigmaScreened;
  end

fclose(fout);

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These are the input files