The code adds some completely useless invisible (or rather white) stuff. The lines
\clip(0pt,403pt) -- (389.957pt,403pt) -- (389.957pt,99.6166pt) -- (0pt,99.6166pt) -- (0pt,403pt);
\color[rgb]{1,1,1}
\fill(3.76406pt,399.236pt) -- (380.923pt,399.236pt) -- (380.923pt,253.19pt) -- (3.76406pt,253.19pt) -- (3.76406pt,399.236pt);
\fill(53.4497pt,394.719pt) -- (374.901pt,394.719pt) -- (374.901pt,289.325pt) -- (53.4497pt,289.325pt) -- (53.4497pt,394.719pt);
draw a white background that is larger than the actual picture. TikZ sees that and thinks it is part of the picture. Simply removing/uncommenting these lines removes most of the whitespace.
Near the end of the first scope,
\color[rgb]{1,1,1}
\fill(3.76406pt,249.426pt) -- (386.193pt,249.426pt) -- (386.193pt,103.381pt) -- (3.76406pt,103.381pt) -- (3.76406pt,249.426pt);
does the same.
Additionally (near the end of the second scope
),
\pgftext[center, base, at={\pgfpoint{220.95pt}{106.392pt}}]{\sffamily\fontsize{9}{0}\selectfont{\textbf{ }}}
adds a blank node below the picture, again enlarging the bounding box.
Removing all those lines gives a tight bounding box.
As far as I know, TikZ cannot do the cropping for you, as it can't know whether the white stuff is intentional or not (there might for example be a dark background behind the image so that white is visible).
I don't really get the question so I hope this is what you wanted. If you include a full document (such that we copy paste and see the problem on our systems) things are much more easier.
Here, you can change the default setting within a scope but your block
style had a node distance
which was resetting every time it is issued. I've made it 2mm such that we can see the difference easier.
\documentclass[tikz]{standalone}
\usetikzlibrary{arrows,shapes.geometric,positioning}
\begin{document}
\begin{tikzpicture}[decision/.style={diamond, draw, text width=4.5em, text badly centered, node distance=3.5cm, inner sep=0pt},
block/.style ={rectangle, draw, text width=6em, text centered, rounded corners, minimum height=4em, minimum height=2em},
cloud/.style ={draw, ellipse, minimum height=2em},
line/.style ={draw,-latex'},
node distance = 1cm,
auto]
\node [block] (1st) {1st};
\node [block, right= of 1st] (2nd1) {2nd1};
\begin{scope}[node distance=2mm and 10mm]%Here we change it for everything inside this scope
\node [block, above= of 2nd1] (2nd2) {2nd2};
\node [block, below= of 2nd1] (2nd3) {2nd3};
\node [block, right= of 2nd1] (3rd1) {3rd1};
\node [block, above= of 3rd1] (3rd2) {3rd2};
\node [block, above= of 3rd2] (3rd3) {3rd3};
\end{scope}
\node [block, below= of 3rd1] (3rd4) {3rd4};
\node [block, below= of 3rd4] (3rd5) {3rd5};
\path [line] (1st) -- (2nd1);
\path [line] (2nd1) -- (2nd2);
\path [line] (2nd1) -- (2nd3);
\path [line] (2nd2) -- (3rd3);
\path [line] (2nd1) -- (3rd1);
\path [line] (1st) -- (2nd1);
\end{tikzpicture}
\end{document}
Best Answer
UPDATE: Without backgrounds and clip.
ORIGINAL ANSWER: