Strange issue with transparency with vector effects

I've purchased a bunch of illustrator vector effects files from a stock image website. I want to be able to have the effects as .pngs (at a large size) so I can use them easily in photoshop, but whenever I try to get rid of the background behind the effects they appear to lose their transparancy (as you can see in the image). The only way I found to be able to keep the effects looking as they should look, is it I export as .psd file, but then you end up with a folder in photoship with hundreds of subfolders and even my new Mac Mini has issues with just moving the effect across the screen. If I could just flatten the vector effect as a .png file I could manipulate it in photoship no problem, but I've not found anyway to do that. Any ideas? I feel like I'm missing something obvious.