Multidimensional NMR processing can't be limited to the Fourier Transform and the phase correction. The resulting plots are affected by noise, stripes and other artifacts. It is possible and desirable to clean up the spectrum. Most of the work is done with the correction of the base-plane.
It consists into the same algorithms and same dialog used for 1-D baseline correction. There's a difference, though. While the dialog is interactive in 1-D spectroscopy, this is not possible with a 2-D spectrum (it would be too slow). Luckily, in most cases it's enough to use the default parameters, so it's not even necessary to open the dialog: just click the icon for automatic baseline correction.
The default correction consists into a 2nd order polynomial that is applied first along all the rows, then along all the columns. If the starting baseline looks more complicated or more simple, you can try using an higher or a lower degree. If you want an immediate feedback, you can extract a single column (or row) and work with it interactively.
Under the hood, iNMR only performs the corrections along the rows. If you ask the program to correct along the Y or Z axes, it will transpose the matrix. To make things faster, iNMR doesn't set the matrix back into its initial state, so you can find the matrix transposed in the end. If you pass through the dialog, you can decide in which order the corrections are performed: it's the same order in which they are listed, from top to bottom.
To transpose explicitly, either press ⇧-T or open the dialog Format > Axes & Scales, then the panel “Transpose” (only necessary in the 3-D case).
If you still see noise and artifacts after the correction of the baseplane, you can apply the command Process > Remove t1 Noise. Should the problem persist, try with Process > Symmetrize > Square Matrix (provided that the number of points is the same along X and Y). Should the remedy be worse than the problem, don't use Undo command. To go back, choose File > Reload, then click the gears icon twice.
Another option for final, cosmentic, processing is represented by the command Smooth. It is akin to weighting with a gaussian function, but not strictly equivalent. It can be performed, interactively, along the horizontal dimension only (you can transpose the matrix anyway). If there is a peak, or shoulder, that is narrow along the horizontal dimension, it is effectively smoothed out. Large peaks remain, but their shape is rounded. At this writing moment, this kind of processing is not memorized by iNMR.