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Compilation is pretty slow because it will download and compile an entire gcc toolchain, locally install it, and then build the libc (musl) and the single busybox package. It can easily take over 30 minutes on a fairly modern Core i7 with 4C/8T, and take around 4GB of RAM.
$ cd buildroot
$ make nintendo3ds_defconfig
$ make -j$(nproc) all # this will take a lot of time
Copy the output to the linux tree
There will be a rootfs.cpio.gz file in the buildroot/output/images/ directory, this file can then be fed into the kernel tree in order to compile a kernel that will automatically boot into the generated rootfs.
example:
$ cp output/images/rootfs.cpio.gz ~/linux_3ds_source_code/rootfs.cpio.gz
$ ... follow the build instructions in the kernel wiki ...