If you mean "I know the topology and perhaps also branch lengths of a particular tree I'm interested in, and want to turn that into an (e.g. NEWICK format) tree file, whose representation I want to then manipulate in a tree viewer such as Dendroscope or FigTree"
then you could try using Mesquite http://mesquiteproject.org/mesquite/mesquite.html .
It takes some practice to get used to it, but maybe you'll find these notes I've put together on it useful http://www.embl.de/~seqanal/courses/commonCourseContent/usingMesquite.html
Maybe SplitsTree can do what you want... There you can conveniently rotate and move clades/nodes while preserving branch lengths....and more.. It can start with all sorts of formats from distance matrices to PHILIP, nexus asf...