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This work examined the challenges faced by Nigerian university libraries in implementing software regimes in their automation/computerization projects. The study argued that Nigerian university libraries have had a long history of attempts at automating/computerizing their operations, but most have not made appreciable efforts. The major problem has been that of selecting the appropriate software to drive these projects. The specific objectives of this study include: to identify the types of software available in these libraries, to identify the extent of use of the available software, to identify the problems associated with software use in these libraries and to suggest the strategies for sustaining software use in libraries. The descriptive survey research method was adopted for this study. The population consisted of the federal university libraries in the southwest geopolitical zone of Nigeria. The result showed that there was no uniformity in the type of software used in these libraries. Also it was found out that the libraries have each used more than one software in their automation projects. The challenges these libraries have had to overcome to implement a sustainable software regime include, lack of proper planning and evaluation of software before acquisition to lack of knowledge of how to evaluate the software. To overcome the challenges the following strategies were suggested. Study and evaluation of the software before purchase, regular seminar/workshops on software maintenance and collaborating with ICT experts and bodies to identify quality software. A number of recommendations were made to remedy the situation.