We are looking to remove transparencies on images within a pdf document, would we be able to do this using PDFNet SDK? The pdf needs to be processed via document composition tool which does not support transparencies on images.
PDFNet does not offer built-in vector transparency flattening. However, you could use PDFDraw (see http://www.pdftron.com/pdfnet/samplecode.html#PDFDraw) to rasterize PDF pages with transparency and replace the existing pages with rasterized version (e.g. see AddImage sample for how to create a PDF page from a Bitmap).
For discussion on how to determine if a PDF has transparency please see: