How to copy a directory structure but only include certain files (using windows batch files)

You don't mention if it has to be batch only, but if you can use ROBOCOPY, try this:

ROBOCOPY C:\Source C:\Destination data.zip info.txt /E

EDIT: Changed the /S parameter to /E to include empty folders.

An alternate solution that copies one file at a time and does not require ROBOCOPY:

@echo off
setlocal enabledelayedexpansion

set "SOURCE_DIR=C:\Source"
set "DEST_DIR=C:\Destination"
set FILENAMES_TO_COPY=data.zip info.txt

for /R "%SOURCE_DIR%" %%F IN (%FILENAMES_TO_COPY%) do (
    if exist "%%F" (
        set FILE_DIR=%%~dpF
        set FILE_INTERMEDIATE_DIR=!FILE_DIR:%SOURCE_DIR%=!
        xcopy /E /I /Y "%%F" "%DEST_DIR%!FILE_INTERMEDIATE_DIR!"
    )
)

The outer for statement generates any possible path combination of subdirectory in SOURCE_DIR and name in FILENAMES_TO_COPY. For each existing file xcopy is invoked. FILE_INTERMEDIATE_DIR holds the file's subdirectory path within SOURCE_DIR which needs to be created in DEST_DIR.

try piping output of find (ie. the file path) into cpio

find . -type f -name '*.jpg' | cpio -p -d -v targetdir/

cpio checks timestamp on target files -- so its safe and fast.

remove -v for faster op, once you get used to it.