The File Manager User's Guide and Reference
says that it is possible to:
File Manager actions
You can use File Manager to display, edit, update, create, copy, compare, print and erase data. You can manipulate this data as logical units, accessed by the data set name; or as physical units, accessed at each physical disk or tape location. Adding to this capability is an interactive interface that allows you to view data in both TABLE and SINGLE RECORD formats.
When working with data sets, you can:
View, change, sort, copy and print data as unformatted or formatted with copybook or dynamic templates
Perform sophisticated data set comparisons
Find and change data strings in a single data set or in multiple data sets
Create new HFS files or QSAM, VSAM or IAM data sets and data set records
Create REXX procedures for advanced record processing
Use selected DFSORT control statements to control the Data Set Copy and Data Set Print functions
Create batch jobs, REXX procedures or CLISTs to automate tasks
This manual also discusses using File Manager in batch. I suspect everything you want to do can be done in File Manager batch jobs -- but you'll need to read the User's Guide and Reference
for details about how (I don't use File Manager often enough to provide any suggestions). You can work with "binary" (that is, hexadecimal) data in File Manager.