If you re-watch the movie you'll notice one key thing about this effect. The monster is never moving when the eyes flash. So to reproduce what they did in the movie is easy enough. Just create a 'glowing eyes' graphic in Photoshop with alpha channel. Overlay it over your movie and fade it in and out.

But if your subject is moving then, depending on the amount of movement and subject scaling going on you might have to rotoscope it. or you may just be able to take your glowing eyes still and keyframe both position and scale to get what you want.

But when you go back to original movie you'll notice that it's a 'false' effect anyway so consider again whether you really need it. By that I mean, in the movie the monster did not have glowing eyes. The effect was only there to make sure the stupid ones amongst us actually knew there was an invisible monster on screen that they wanted you to be aware. Look again, they only used that juicy invisible cloak effect when they actually wanted the audience to 'see' the invisible monster. There are some shots where he would have been on screen but was completely invisible.

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