You have given us very little to work on. you need to include much more information. Fix the above code to look like this 

########################################
print 'size new:'.scalar(@new)."\n"; 
print 'n_size  :'.$n_size."\n"; 
print 'new     :'.join('|',@new)."\n"; 
########################################

for(my $i=0;$i<$n_size;$i++){
      my  @w= split(/,/ , $new[$i]);

      ########################################
      print 'i       :'.$i."\n"; 
      print 'size w  :'.scalar(@w)."\n"; 
      print 'w       :'.join('|',@w)."\n"; 
      ########################################
     
      $w[0]=~s/\'//;  #pre-process to remove ' from text 
      $w[0]=~s/\'//;    as @w='word1' 'word2'
      $w[1]=~s/\'//;  
      $w[1]=~s/\'//; 

      ########################################
      print 'w[0]    :'.$w[0]."\n"; 
      print 'w[1]    :'.$w[1]."\n"; 
      print 'size w  :'.scalar(@w)."\n"; 
      ########################################
      
      
      my $t1 = "$w[0]";  #$w[0]=word1  without single quotes
      my $t2 = "$w[1]";  #$w[1]=word2

      ########################################
      print 't1      :'.$t1."\n"; 
      print 't2      :'.$t2."\n"; 
      ########################################
     
#      print $t1,$t2,"__________";   #working
      
     my $cu1 = $umls->getConceptList($t1); #calling function from umls
+::similarity #ERRRO 1 as mentioned

      ########################################
      print 'raw  cu1:'.$cu1."\n"; 
      print 'size cu1:'.scalar(@{$cu1})."\n"; 
      print 'cu1     :'.join('|',@{$cu1})."\n"; 
      ########################################

      my $cui1 =pop @{$cu1};

      ########################################
      print 'new  cu1:'.$cu1."\n"; 
      ########################################

      my $cu2 = $umls->getConceptList($t2);***error

      ########################################
      print 'raw  cu2:'.$cu2."\n"; 
      print 'size cu2:'.scalar(@{$cu2})."\n"; 
      print 'cu2     :'.join('|',@{$cu2})."\n"; 
      ########################################

      my $cui2 = pop @{$cu2};

      ########################################
      print 'new  cu2:'.$cu2."\n"; 
      ########################################

#      print $cui1;    # ****ERROR2 unintialized $cui1
      my $lvalue = $lch->getRelatedness($cui1, $cui2); 
      my $value = $path->getRelatedness($cui1, $cui2);

[download]
Then run it and post the output. Then someone may be able to help you.

In reply to Re: Use of uninitialized value $cui1 in print by huck
in thread Use of uninitialized value $cui1 in print by Raksha Jalan

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