G'day littlewenwen,

Welcome to the monastery.

One way to do that is with Tie::File:

$ cat > fred.dat
abcd    123     456     defg
cdefg   23              as
        345     235     
xsd             swe
[download]

$ perl -Mstrict -Mwarnings -e '
    use Tie::File;
    tie my @fred_data, q{Tie::File}, q{fred.dat} or die $!;
    @fred_data = map { s/(^|\t)(?=\t|$)/${1}Missing/g; $_ } @fred_data
+;
    untie @fred_data;
'
[download]

$ cat fred.dat
abcd    123     456     defg
cdefg   23      Missing as
Missing 345     235     Missing
xsd     Missing swe     Missing
[download]