The perl code is calling out to the shell with the system command. It's using interpolation to inject the value of the perl variables $label, $apex, $reference, and $name into the string that will be executed by the shell.

The output of the awk command will be captured in a file named temp_marker_$name, where $name is first expanded to whatever is held in that perl variable

The purpose of the the backslashes in the string is to ensure that the following character is passed literally to the shell. For example, this prevents perl from treating constructs such as "$3" as a perl variables.