Facility　layout　design　is　an　essential　planning　task　to　resolve　potential　spatial　conflicts　and　overlapping　during　practical　operations.　A　discretized　cell　optimization　model　is　developed　to　optimize　site　space　usages.　Site　areas　and　facilities　are　represented　by　small　unit　cells　to　effectively　model　irregularities,　and　the　availability　of　unit　cells　for　use　in　a　facility　setup　is　modeled　by　binary-type　variables.　With　size　and　shape　requirements　through　linear　constraints,　the　site　layout　design　can　be　formulated　as　a　binary　mixed　integer-linear　programming　(BMILP)　problem　to　allocate　different　facilities　onto　different　site　available　areas　in　optimal　shapes　and　locations.　Total　material　transportation　costs　across　facilities　are　optimized　subject　to　various　design　constraints　ensuring　safety,　homogenous　facility　setups,　physical　size,　and　orientation　requirements.　The　proposed　cell　model　is　verified　by　comparing　optimization　results　with　results　obtained　by　conventional　point　notation　methods.　A　standard　branch-and-bound　algorithm　is　applied　to　solve　a　global　optimal　solution,　and　the　numerical　example　is　optimized　for　illustrating　the　very　different　optimized　layout　plan　in　terms　of　facility　locations,　positions　of　entry　and　exit　points,　shapes,　and　orientations　of　different　facilities.　(C)　2016　American　Society　of　Civil　Engineers.