How to remove duplicate lines in file with TCL

Your code actually seems to work with a minor change:

set in [open file.txt r]
array set seen {}
while {[gets $in line] != -1} {
     blank lines should be printed as-is
    if {[string length [string trim $line]] == 0} {
        puts $line
        continue
    }

     create the "key" for this line
    regsub {\mPoint \d+} $line {} key
    regsub {\mcolor=\w+} $key {} key

     print the line only if the key is unique
    if { ! [info exists seen($key)]} {
        puts $line
        set seen($key) true
    }
}
close $in

If you didn't care about the order presented or the blank lines, you could simply use a list function:

set file [open file.txt r]
set read [lsort -unique [read $file]]
foreach x $read { puts $x }