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To get unique results you could just run everything throught sort -u:
grep -xFf file1 file2 | sort -u
or
awk 'NR==FNR{A[$1]; next}$1 in A' file1 file2 | sort -u



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Alternatively, one...

You can also try like this

1st sort both the files

sort filename1 -o filename1
sort filename2 -o filename2

then try

comm -12 filename1 filename2

If I run both scripts on your sample:


$ cat file1
Milestone1
Milestone2
Milestone3
Milestone4
Milestone5
Milestone6
$ cat file2
Milestone1
Milestone12
Milestone13
Milestone14...

You would need to redirect the output:
grep -xFf file1 file2 > file3

An alternative would be:
awk 'NR==FNR{A[$1]; next}$1 in A' file1 file2 > file3

Hi, try:
grep -xFf file1 file2