How to get the corrected matrix after SVA batch effect correction
If you want to plot the "corrected" expression, you will need to remove the variation introduced by these surrogate variables. Removing the expression affected can introduce some bias too and it is usually not recommended (despite comBat doing so). You should apply linear algebra, you can look at here is an example how to do it:

library("corpcor")
s &lt;- corpcor::fast.svd(t(scale(t(dat), center = TRUE, scale = TRUE)))
pcSds &lt;- s$d
pcSds[1] &lt;- 0
svdexp &lt;- s$u %*% diag(pcSds) %*% t(s$v)
colnames(svdexp) &lt;- colnames(dat)


But if your surrogate variables do have a big enough influence on your MDS plot to be observable (IMHO) there would be too much batch effect to work with the data.