The documentation for HTML::TableExtract gives you an example using the tree option:

# Example: Extracting as an HTML::Element tree structure
 # Rather than extracting raw text, the html can be converted into a
 # tree of element objects. The HTML document is composed of
 # HTML::Element objects and the tables are HTML::ElementTable
 # structures. Using this, the contents of tables within a document ca
+n
 # be edited in-place.

 use HTML::TableExtract qw(tree);
 $te = HTML::TableExtract->new( headers => qw(Fee Fie Foe Fum) );
 $te->parse_file($html_file);
 $table = $te->first_table_found;
 $table_tree = $table->tree;
 $table_tree->cell(4,4)->replace_content('Golden Goose');
 $table_html = $table_tree->as_HTML;
 $table_text = $table_tree->as_text;
 $document_tree = $te->tree;
 $document_html = $document_tree->as_HTML;
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