If you're talking about the surface of a colony of fungus, and it is not flat, there are many different terms you could use based on the level of "not-flat-ness" (patent pending):
- Rough - Think like the texture of sandpaper or jeans
- Ribbed - Like corduroy pants
- Varied - Like rolling hills. Areas are flat, and others sloped
- Sloped - Like a round hill, or the top of a mushroom
- Cracked - Has cracks in it
- Creviced - Like cracked, but deeper
- Undulating - Marked by steep rolling hills
- Pockmarked - Filled with small holes, like a sponge
- Fissured - Similar to cracked, but stronger
- Craggy - Like the rocky face of a cliff
- Cleft - Split in the middle, like a cleft chin
- Mountainous - Mountains
- Severe - Steep
- Pitted - Like pockmarked, but deeper holes
- Not flat - Exactly what it says, something's not flat.
They all have subtle meanings, implying different levels of "not-flat-ness."
Also, as others have pointed out, you would not usually say that something is both flat AND rugged. In English, rugged is typically used to amplify the adjective describing how unflat something is. So mountains are rugged, but a flat plains land probably wouldn't necessarily be, unless you're trying to imply that at first glance the prairie looked flat and easy to cross but it turned out not to be because it was full of danger.