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How to convert physical memory into virtual memory using CR3 if my program is a PE file and that's why can't read physical address of page directory at CR3 register?

You access physical memory by mapping a logical address to a physical page and then accessing the memory through that address. You are pretty free to choose whatever address you like to represent the physical page.

How to read the physical address of Page Directory in a PE file?

You seem to have missed some concepts.

The physical address of a process's PD (i.e. the value that gets written to CR3) is decided by the OS's low level memory manager (usually, it just grabs the first free page and uses that). It is not stored in the executable file, nor should the executing process care about it (in fact, processes rarely need to care that the addresses they're using are not actually physical addresses) as it is a kernel-level detail.

This should be in OS Development, not General Programming.

And that should go under report post. Although I think autodelete or the moderator archives is a much better place with this OP considering his consistent bad questions and complete lack of followup, as if he does not want to be helped.

What is teh virtual address of page directory in CR3?