I don't think you need the eqnarray environment at all. Instead, embed the cases (or, as shown in the example below, a dcases) environment inside an ordinary equation environment.

\documentclass{article}
\usepackage[a4paper,margin=2.5cm]{geometry} % choose paper size and margins
\usepackage{mathtools} % for 'dcases' environment
\def\flen{\bar{F}^\mathrm{M}_{\mathrm{len}}}
\def\finv{{(\bar{F}^{\mathrm{M}}_{\mathrm{V}}})^{-1}}
\begin{document}
\begin{equation}
\finv(F^{\mathrm{CE}},F^\mathrm{a})=
\begin{dcases}
\frac{F^{\mathrm{CE}}}{\varepsilon}\left(\frac{\varepsilon-F^{\mathrm{a}}}{F^{\mathrm{a}}+\varepsilon/A_{\mathrm{f}}+\xi}+{\frac{F^\mathrm{a}}{F^\mathrm{a}+\xi}}\right) - \frac{F^\mathrm{a}}{F^\mathrm{a}+\xi}\,, & \phantom{0\le{}} F^{\mathrm{CE}} <0 \\[1.5ex]
\frac{F^{\mathrm{CE}}-F^\mathrm{a}}{F^{\mathrm{a}}+F^{\mathrm{CE}}/A_{\mathrm{f}}+\xi}\,, & 0 \leq F^{\mathrm{CE}} <F^\mathrm{\mathrm{a}} \\[1.5ex]
\frac{F^{\mathrm{CE}}-F^\mathrm{a}}{\dfrac{{(2+2/A_{\mathrm{f}})}{(F^\mathrm{a}\flen - F^{\mathrm{CE}})}}{\flen - 1}+\xi}\,, & F^\mathrm{a} \leq F^{\mathrm{CE}} < 0.95F^\mathrm{a}\flen \\[1.5ex]
f_{v_0} + \frac{F^{\mathrm{CE}} - 0.95F^\mathrm{a} \flen }{\varepsilon F^\mathrm{a} \flen}(f_{v_1} - f_{v_0})\,, & 0.95F^\mathrm{a} \flen \leq F^{\mathrm{CE}}
\end{dcases}
\end{equation}
\end{document}
Addendum: If you want the conditioning statements to feature exact alignments on the inequalities, it turns out to be easier to use an array environment instead of a dcases environment. Personally, I don't think the result looks better than what's achieved above (i.e., with a dcases environment and less than perfect alignment of the inequalities). In case you're curious: the @{}>{{}}c<{{}}@{} constructs serve to center-set the ineqality symbols while assigning the proper amount of whitespace to their left and right.

\documentclass{article}
\usepackage[a4paper,margin=2.5cm]{geometry} % choose paper size and margins
\usepackage{amsmath} % for \dfrac macro
\usepackage{array}
\def\flen{\bar{F}^\mathrm{M}_{\mathrm{len}}}
\def\finv{(\bar{F}^{\mathrm{M}}_{\mathrm{V}})^{-1}}
\begin{document}
\begin{equation}
\finv(F^{\mathrm{CE}},F^\mathrm{a})=
\left\{
\begin{array}{ >{\displaystyle}l @{\quad} r @{}>{{}}c<{{}}@{} c @{}>{{}}c<{{}}@{} l @{} }
\frac{F^{\mathrm{CE}}}{\varepsilon}\left(\frac{\varepsilon-F^{\mathrm{a}}}{F^{\mathrm{a}}+\varepsilon/A_{\mathrm{f}}+\xi}+{\frac{F^\mathrm{a}}{F^\mathrm{a}+\xi}}\right) - \frac{F^\mathrm{a}}{F^\mathrm{a}+\xi}\,,
& & & F^{\mathrm{CE}}& <&0 \\[4ex]
\frac{F^{\mathrm{CE}}-F^\mathrm{a}}{F^{\mathrm{a}}+F^{\mathrm{CE}}/A_{\mathrm{f}}+\xi}\,,
& 0 &\leq& F^{\mathrm{CE}} &<&F^\mathrm{\mathrm{a}} \\[4ex]
\frac{F^{\mathrm{CE}}-F^\mathrm{a}}{\dfrac{{(2+2/A_{\mathrm{f}})}{(F^\mathrm{a}\flen - F^{\mathrm{CE}})}}{\flen - 1}+\xi}\,,
& F^\mathrm{a} &\leq& F^{\mathrm{CE}} &<& 0.95F^\mathrm{a}\flen \\[7ex]
f_{v_0} + \frac{F^{\mathrm{CE}} - 0.95F^\mathrm{a} \flen }{\varepsilon F^\mathrm{a} \flen}(f_{v_1} - f_{v_0})\,,
& 0.95F^\mathrm{a} \flen & \leq & F^{\mathrm{CE}} \\
\end{array}\right.
\end{equation}
\end{document}
eqnarrayvsalign... – Werner Feb 03 '15 at 18:59\finvand\flen? – Bernard Feb 03 '15 at 19:10