From what I know its the effect of breaking symmetry and oscillations appearance due to that you have finite grid in you simulations. 

Check for example http://departments.icmab.es/leem/siesta/Documentation/Manuals/siesta-3.1-manual/node47.html

The eggbox effect is the breakdown of translational invariance.  In DFT, you are trying to find a representation of a continuously varying quantity (the electron density) by plotting points on a discrete grid and then fitting a function through them.  If the density varies slowly, everything is simple.  Wherever you put the origin of your grid, the final fitted function will be the same.

However, if the density varies rapidly, when compared with the grid spacing, then a small change in the position of the grid origin can produce a large change in the output function (and its integral).

As an example, compare the following two discretisations of the same function:

https://agendafisica.files.wordpress.com/2011/02/sample1.png?w=570

https://agendafisica.files.wordpress.com/2011/02/sample2.png?w=570

(taken from https://agendafisica.wordpress.com/2011/02/03/the-eggbox-effect-explanation-for-idiots/)

There are a number of solutions, and which one is most appropriate depends on the details of your simulation.  You can use a finer grid, you can use a Fourier transform to remove high (spatial) frequency components from the electron density or you can perform the calculation for a number of different grid positions and average the result.

Here you can find a very helpful tutorial of Siesta3.2. Look at the chapter 5 (Converging the simulations) at point 4 ( Convergence of the calculation with respect the MeshCutoff. The eggbox effect. ). You'll find a brief explanation of Eggbox effect in Siesta.

http://personales.unican.es/junqueraj/JavierJunquera_files/Metodos/Hands-on-session.html

The FilterCutoff should be similar or lower than the Mesh.Cutoff to avoid the eggbox effect on the atomic forces. However, one should not try to converge Mesh.Cutoff while simultaneously changing FilterCutoff , since the latter in fact changes the used basis functions.