WSC_SL My first thought here is to filter the the file names so you're only reading the ones you want to work with, then after the Multi-File Reader Snap, add a Binary Router so you can branch the files down different pathways for transformation depending on the file name. After the Binary Router you can use the Pipeline Execute Snap with the input view type changed from "Document" to "Binary".
Here is a screenshot example:
Here is a Pipeline Execute with 'input0' changed from "Document" to "Binary" using the 'Type' drop-down box:
