TIMTOWTDI

test.sh:

#!/bin/sh
cat $1 | while read var1 do

    var2=`perl -e 'system("echo $ARGV[0]")' $var1`

    rm -r $var2

done

a.txt:

$ENV_VAR1/foo/
$ENV_VAR2/bar
$ENV_VAR3/foo/bar

test.sh a.txt