It depends on what you call a "flow chart." If the flowchart is a simple view, i.e. a directed graph, where no node points up (to a node that you may have previously visited), then what you described is a tree whose nesting in the plane is trivial.
If, however, your block diagram has cycles (cycles), then simply build a counterexample, a graph that does not fit into the plane. For a far-fetched example (since no restrictions were specified), consider the full K5 graph in which each node is connected to all the others. This chart is not flat.
As for drawing graphs, I would recommend the excellent GraphViz tool, which attracts (among other things) beautiful flowcharts with automatic layout. You can choose a rendering engine that tries to preserve some order in your chart, and there is an explicit option for hierarchical charts.
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