cut with 2 character delimiter

awk's field separator is treated as a regexp as long as it's more than two characters. .. as a regexp, means any 2 characters. You'd need to escape that . either with [.] or with \..

awk -F'[.][.]' ...
awk -F'\\.\\.' ...

(the backslash itself also needs to be escaped (with some awks like gawk at least) for the \n/\b expansion that the argument to -F undergoes).

In your case:

awk -F' +|[.][.]' '/^[^#]/{print $1}' < output.txt

In any case, avoid shell loops to process text, note that read is not meant to be used like that, that echo should not be used for arbitrary data and remember to quote your variables.

Sample test script that works for me:

#!/bin/sh

raw="1F3C6..1F3CA
1F3CF..1F3D3
1F3E0..1F3F0"

for r in $raw
do
    f1=`echo "${r}" | cut -d'.' -f1`
    f2=`echo "${r}" | cut -d'.' -f2`
    f3=`echo "${r}" | cut -d'.' -f3`
    echo "field 1:[${f1}] field 2:[${f2}] field 3:[${f3}]"
done

exit

And the output is:

field 1:[1F3C6] field 2:[] field 3:[1F3CA]
field 1:[1F3CF] field 2:[] field 3:[1F3D3]
field 1:[1F3E0] field 2:[] field 3:[1F3F0]

Edit

After reading Stéphane Chazelas comment and linked Q&A, I re-wrote the above to remove the loop.

I could not work out a way to remove the loop and keep the parts as variables (for example; $f1, $f2 and $f3 in my original answer) that could be passed around. Still I don't know what was required output in the original question.

First, still using cut:

#!/bin/sh
raw="1F3C6..1F3CA
1F3CF..1F3D3
1F3E0..1F3F0"

printf '%s\n' "${raw}" | cut -d'.' -f1,3

Which will output:

1F3C6.1F3CA
1F3CF.1F3D3
1F3E0.1F3F0

Could replace the displayed . with any string using the --output-delimiter=STRING.

Next, with sed instead of cut in order to give more control of the output:

#!/bin/sh
raw="1F3C6..1F3CA
1F3CF..1F3D3
1F3E0..1F3F0"

printf '%s\n' "${raw}" | sed 's/^\(.*\)\.\.\(.*\)$/field 1 [\1] field 2 [\2]/'

And this will render:

field 1 [1F3C6] field 2 [1F3CA]
field 1 [1F3CF] field 2 [1F3D3]
field 1 [1F3E0] field 2 [1F3F0]

You could use IFS to split each line discarding the field between the two dots:

#/bin/sh
while IFS=\. read a _ b
do
     echo "field one=[$a] field two=[$b]"
done < "file"

Execute:

$ ./script
field one=1F3C6 field two=1F3CA
field one=1F3CF field two=1F3D3
field one=1F3E0 field two=1F3F0

Assuming that file is:

$ cat file
1F3C6..1F3CA
1F3CF..1F3D3
1F3E0..1F3F0