classicthesis uses the package typearea, which tries to preserve a general aspect when changing the text block (check the Chapter 2 in the KOMA-Script Guide for the motives (See also this answer to How to configure KOMA classes such that the bottom margin of a page equals its top margin?) The text block is defined in classicthesis (when not using minion option) as:
\areaset[current]{336pt}{750pt} % ~ 336 * factor 2 + 33 head + 42 \the\footskip
Following a sugestion within classicthesis.sty, a good proportion for Palatino 11pt would be 336 × 705pt, which results in a sort of vertically symmetrical text block. A MWE:
\documentclass[11pt]{book}
\usepackage{classicthesis}
\usepackage{blindtext,layouts}
\areaset[current]{336pt}{705pt}% as suggested in classicthesis.sty, line 273
\begin{document}
\blindtext[6]\footnote{blindtext}
\begin{figure}
\currentpage
\pagediagram% To check the layout and lengths
\pagevalues
\end{figure}
\end{document}
Another option would be to call geometry: as stated in the first comment to What packages are incompatible with KOMA-Script?, "geometry resets the from typearea calculated margins if you don't use the option pass (for showframe)". We lose the automatic calculated margins, therefore we lose the aspect, but it is possible. A MWE:
\documentclass[11pt]{book}
\usepackage{classicthesis}
\usepackage{blindtext,layouts}
\usepackage[top=48pt,bottom=48pt,textwidth=336pt]{geometry}
\begin{document}
\blindtext[6]\footnote{blindtext}
\begin{figure}
\currentpage
\pagediagram% To check the layout and lengths
\pagevalues
\end{figure}
\end{document}
classicthesisuses the packagetypearea(from the KOMA-Script bundle), you should check the Chapter 2 in the KOMA-Script Guide – henrique Sep 20 '12 at 17:18