Tao,

You might look into the capabilities of ghostscript. It should be installed with your LaTeX install (MacTeX or equivalent), but if not, you can install it using Homebrew via brew install gs. Specifically, ghostscript should install a utility called ps2pdf that (IIRC) produces clean PDF files from an input EPS.

FYI, the following MWE worked on my system using TextMate 2.0-beta6.8. Note that the order in which graphicx and epstopdf are loaded is important.

\documentclass{article}
\usepackage{graphicx,epstopdf}
\begin{document}
A sample figure:
\begin{figure}[h]
    \centering
        \includegraphics[width=.9\textwidth]{Figures/sample.eps}
    \caption{caption}
    \label{fig:sample}
\end{figure}

     
\end{document}