EMF is not going to produce good results. It mainly works with Office applications, not page layout.
Try converting to transparent PNGs but open them in Photoshop and resave them. I've never had problems with PNGs from Photoshop.
There is more than one format of TIFF and the export filter is probably not preserving the transparency.
If the original files are vector based, converting them to a bitmap format means they'll lose quality.
Can you convert them to something like PDF or EPS? That ought to work far better.
1 person found this helpful
I've made Chemistry Books since 14 years with thousands images files created by authors in Chemdraw!
Eps Chemdraw export is a good format (for me)! (including a really cool possibility to have play between Chem and Illustrator with a dynamic link between fonts sizes and length of atomic bonds!