This paper deals with the sub-problems of generating a mask pattern from the logical description of a large-scale CMOS circuit. The large-scale layout can be generated in divide-and-conquer style: divide a given circuit into a set of sub-circuits, generate the layout of each sub-circuit, and merge the resulting layouts to create the whole layout. This paper proposes a layout synthesis algorithm for a sub-circuit with physical constraints for the synthesis scheme above. The physical constraints considered here are the relative placement of logic cells (sets of logic gates) and the routing constraint based on the costs of wiring layers and vias. These constraints will be given by the global optimizer in a two-dimensional layout synthesis routine, and they should be kept at the subsequent one-dimensional layout synthesis for a sub-circuit. The latter is also given for enhancing the circuit performance by limiting the usage of wiring layers and vias for special net such as a clock net. The placement constraint is maintained using PQ-tree, a tree structure representing a set of restricted permutations of elements. One-dimensional layout synthesis determines the placement of transistors by the enhanced pairwise exchanging method under the PQ-tree representation. The routing constraints is considered in the newly developed line-search routing method using a cost-based searching. Experimental results for practical standard cells, including up to 200 transistors, prove that the algorithms can produce the layouts comparable to handcrafted cells. Also on a two-dimensional layout synthesis using the algorithms, the results for benchmark circuits of Physical Design Workshop 1989, i.e., MCNC benchmark circuits, are superior to the best results exhibited at Design Automation Conference 1990.