Recently, many big libraries all over the world have been scanning their collections to make them publicly available and to preserve historical documents. We present a modular software system which can be used as a tool for semi-automatical processing of historical handwritten Arabic documents. The development of this system is part of the HADARA project which aims for historical document analysis of Arabic manuscripts and consists of a project team including engineers and computer scientists but also users such as linguists and historians. The HADARA system is designed to support script and content analysis, identification, and classification of historical Arabic documents. The system has been created following an iterative development approach, and the current version assists the user in an interactive and partially already in an automatic manner. In this paper, a system overview is given and the first modules are presented which support the annotation of a scanned manuscript in a semi-automatic manner. They comprise page layout analysis, text line segmentation, and transcription. Word spotting is the first application implemented in the HADARA system and its concept is outlined in this paper.