To negate the \perp
(perpendicular) symbol, the command \not\perp
provides a simple solution, but this negated symbol doesn't look that great IMHO:

If you load the mathabx
package, you get the command \notperp
which looks pretty good, as does now the output of \not\perp
. The same effect can be achieved if you load either the MnSymbol
package or the fdsymbol
package and use the command \notperp
(same name used by both packages). Notice, though, that even if you load the MnSymbol
of the fdsymbol
package, the output of \not\perp
still looks pretty bad, i.e., as bad as if you hadn't loaded any extra package at all.
Addendum: Following a request by the OP, here's an MWE that shows how to load the mathabx
package and generate the symbol using the package's \notperp
macro, as well as with \not\perp
"
\documentclass{article}
\usepackage{mathabx}
\begin{document}
$a \notperp b$, $c \not\perp d$
\end{document}

Next, here's an MWE that shows the use of the MnSymbol
package to generate these symbols:
\documentclass{article}
\usepackage{MnSymbol}
\begin{document}
$a \nperp b$, $c \not\perp d$
\end{document}

Finally, with the use of the fdsymbol
package and its \nperp
macro:
\documentclass{article}
\usepackage{fdsymbol}
\begin{document}
$a \nperp b$, $c \not\perp d$
\end{document}

Happy TeXing!
Ah well it all depends.
In the default setup as commented in the linked question they are the same symbol but with different mathclass (so different spacing) \bot
is a mathord (like an ordinary letter) and \perp
is a relation (like <
). Relations get more space either side if used between two symbols but in M^{\perp}
the mathlist that forms the superscript only has one atom, so there is no additional spacing applied. That means that M^\bot
and M^\perp
produce identical output.
You could argue that \bot
was better as it is naturally a symbol and a relation is not intended here.
Or you could argue that \perp
is better as bot refers to a logical notion of bottom/false whereas perp refers to perpendicular which is somehow semantically related to orthogonal.
Or you could argue that they make identical output so it makes no difference and you can use either.
Best Answer
To summarize the comments, here are the options currently available.
The

mathabx
provides\obot
and\bigobot
. These symbols look likeIf you don't want to include all the
mathabx
symbols (they overwrite many Computer Modern symbols), then you can use the following setup (taken from Importing a Single Symbol From a Different Font):Unicode additionally defines ⦹ U+29B9 (circled perpendicular), but doesn't provide a big counterpart. The symbol can be used with the

unicode-math
package and LuaLaTeX or XeLaTeX. As of summer 2012 only the XITS and Cambria math fonts include the symbol. In XITS Math it looks likeThe corresponding TeX code is
The Unicode also has

\obot
, looking similar to the example above, but doesn't provide\bigobot
. You could try to fake the large symbols with something like{\text{\Large$\operp$}}\limits_{i∈I} V_i
, but the scaling will make the symbol heavier:The STIX fonts LaTeX package is available, but not yet in TeX Live (as of this writing). After installing it you can use (with normal pdfLaTeX)
to get an output similar to the above.
If you only want the
\operp
symbol from STIX, you can set it up yourself:In general have a look at How to look up a symbol or identify a math symbol or character? to see how you can find a specific symbol.