Hi Shash,
Your desired output doesn't make any sense to me. When you find lines in both files for a given key, the data from the fields in both files are intermixed. When data is only found in one file, why isn't the output supposed to have the data from each field in that input file in the output columns related to those input fields. In other words, with your sample input data, why isn't the output:

Code:

Cu1L1B1L2B2
Cu2L1  L2  
Cu3L1B1L2B2

instead of the output you said you want:

Code:

Cu1L1B1L2B2
Cu2L1L2    
Cu3L1B1L2B3

especially since there is no B3 anywhere in either of your sample input files?

To get the output shown above, you could use something like:

Code:

awk '
FNR == NR {
	data1[key = substr($0, 1, 3), 1] = substr($0, 8, 2)
	data1[key, 2] = substr($0, 10, 2)
	keys[key]
	next
}
{	data2[key = substr($0, 1, 3), 1] = substr($0, 4, 2)
	data2[key, 2] = substr($0, 6, 2)
	keys[key]
}
END {	for(key in keys)
		printf("%s%2.2s%2.2s%2.2s%2.2s\n", key, data1[key, 1],
		    data2[key, 1], data1[key, 2], data2[key, 2])
}' file1.txt file2.txt > output.txt

but note that the order of the output lines may vary. If the output order matters, you need to clearly state how the output order should be determined when:Note that I asked what operating system you're using and you didn't answer.

If you're using a Solaris/SunOS system and want to try the above code, change awk to /usr/xpg4/bin/awk or nawk.

The missing 2nd components of the 2nd data1[] and data2[] assignments have been fixed as noted by RudiC in post #5.