This question already has an accepted answer, but a bit of elucidation on the Unix file hierarchy seems to be in order. Everybody who first encounters the Unix file hierarchy wants to change it, not even excepting ex-CEO Steve Jobs (tip o'the hat in his general direction). The layout has been codified for Linux in the so called FHS (Filesystem Hierarchy Standard), which lays out the location and purpose for each of the typical system directories. Wikipedia has a concise listing of some these. The Linux Standard Base (LSB) goes further and outlines the APIs that must be present on an LSB-compliant system, part of which is specified by the FHS.
The Unix way is to isolate Unix system files from administrator files and further both of these from user files. The user is typically permitted to use his or her home directory (usually in the /home directory structure), /tmp, /var/tmp and certain specific files that the system may permit by design or administrator configuration.
The administrator typically has control over the system, but the FHS reserves a handful of directories for the administrator. Specifically, /usr/local and /opt (including some other related directories) are reserved by the system for administrator use. These are used to install software that is not maintained by or provided by the system.
The Linux system, which today is maintained and managed by the creator of the distro used, reserves most of the rest of the filesystem hierarchy for itself. This division of responsibilities helps maintain the security and stability of the system. When necessary, modifications may be made by either the administrator or the package system (if any) of the distro. Popular package systems include Debian's apt, Novell's zypper, RedHat's yum or Gentoo's portage package manager. Most of these package managers have means for the administrator to control the selection, configuration and maintenance of system packages.
In conclusion, an application programmer should keep in mind that the user has limited access on the system and for good reason. Messing with system directories is likely not the right direction, unless for one of the purposes outlined in the FHS.
If changes must be made, there are tools available to work around the situation, including judicious use of sudo, PolicyKit, ACLs and file attributes (chmod, etc.).
The original author has not explained the purpose for the directory he needs, so it is hard to answer more specifically. I hope this answer is useful.