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You can create a script outside ISE/Modelsim to create the macro file. In this macro file use the "add wave" to select signals you want to view in Modelsim waveform viewer.
From within Modelsim you can also create this macro file: select all signals you want to view in the waveform viewer. In the waveform viewer select File > Save. By default it saves the macro file to wave.do. When you open Modelsim again you can load this wave.do by selecting File > Load in Modelsim waveform viewer. This saves you time by selecting the same signals again (and again) in Modelsim.
But you can create this macro file also with any script language (Tcl, Perl, ...). The only thing you have to know is the exact path of the signal you want to view and the options for the "add wave" command.