State machines are good, but I don't think you need one here, because:

• All comment lines start with 'c'
• You don't need to look at a previous line to see if you're in the 'm' state. Unless the line starts with 'c', you are

Try this, after you've opened input file. (Nice job on using the 3 arg form of open, and using warnings and strict btw)

while (<$FILE>){    # Don't need to use a $line variable; leave it in 
+$_
    next if /^c\s/;   # Skip comments
 
    $_ = (split /\$/)[0]  # Throw away everything to the right of $ (i
+f any)

      # I'm not sure from your description if this is the pattern you 
+want; I'm guessing
    foreach my $datum (/ (\w+\.\w\wc) /gx ){  
       push(@data, $datum)}}       # This could be made terser
[download]

I'm assuming that all comment lines start with a 'c' and aren't continued.

BTW, having an both an array and a scalar named 'array' is confusing and unnecessary. In your code

        $array=@array;
        for ( $i=1; $i<$array; $i=$i+2)
[download]

Better to just say

    for ( $i=1; $i < @array; $i=$i+2)
[download]

The '<' puts @array in a scalar context, so $i is compared to the length of @array.

Tell us how it goes
throop

Code not tested

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